Reliability Of Alphafold Vs Experimental Structure

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Paper One substrate many enzymes virtual screening uncovers missing genes of carnitine biosynthesis in human and mouse.

Malatesta, Marco; Fornasier, Emanuele; Di Salvo, Martino Luigi et al. · 2024 · Nature communications · DOI

Full title: One substrate many enzymes virtual screening uncovers missing genes of carnitine biosynthesis in human and mouse.

Authors: Malatesta, Marco; Fornasier, Emanuele; Di Salvo, Martino Luigi; Tramonti, Angela; Zangelmi, Erika; Peracchi, Alessio; Secchi, Andrea; Polverini, Eugenia; Giachin, Gabriele; Battistutta, Roberto; Contestabile, Roberto; Percudani, Riccardo

Year: 2024

Venue: Nature communications

DOI: https://doi.org/10.1038/s41467-024-47466-3

Paper Deep contrastive learning enables genome-wide virtual screening

Yinjun Jia, Bowen Gao, Jiaxin Tan, Jiqing Zheng, Xin Hong, Wenyu Zhu, Haichuan Tan, Yuan Xiao, Liping Tan, Hongyi Cai, Yanwen Huang, Zhiheng Deng, Xiangwei Wu, Yue Jin, Yafei Yuan, Jiekang Tian, Wei He, Weiying Ma, Yaqin Zhang, Wei Zhang, Lei Liu, Chuangye Yan, Yanyan Lan · 2025 · bioRxiv · DOI

Full title: Deep contrastive learning enables genome-wide virtual screening

Authors: Yinjun Jia, Bowen Gao, Jiaxin Tan, Jiqing Zheng, Xin Hong, Wenyu Zhu, Haichuan Tan, Yuan Xiao, Liping Tan, Hongyi Cai, Yanwen Huang, Zhiheng Deng, Xiangwei Wu, Yue Jin, Yafei Yuan, Jiekang Tian, Wei He, Weiying Ma, Yaqin Zhang, Wei Zhang, Lei Liu, Chuangye Yan, Yanyan Lan

Year: 2025

Venue: bioRxiv

DOI: https://doi.org/10.1101/2024.09.02.610777

Paper TopoFormer: Multiscale Topology-enabled Structure-to-Sequence Transformer for Protein-Ligand Interaction Predictions

Wei, Guo‐Wei, Chen, Dong, Liu, Jian · 2024 · DOI

Full title: TopoFormer: Multiscale Topology-enabled Structure-to-Sequence Transformer for Protein-Ligand Interaction Predictions

Authors: Wei, Guo‐Wei, Chen, Dong, Liu, Jian

Year: 2024

DOI: https://doi.org/10.21203/rs.3.rs-3640878/v1

Paper Revolutionizing Medicinal Chemistry: The Application of Artificial Intelligence (AI) in Early Drug Discovery

Han, Ri, Yoon, Hongryul, Kim, Gahee, Lee, Hyundo, Lee, Yoonji · 2023 · Pharmaceuticals · DOI

Full title: Revolutionizing Medicinal Chemistry: The Application of Artificial Intelligence (AI) in Early Drug Discovery

Authors: Han, Ri, Yoon, Hongryul, Kim, Gahee, Lee, Hyundo, Lee, Yoonji

Year: 2023

Venue: Pharmaceuticals

DOI: https://doi.org/10.3390/ph16091259

Paper Machine Learning Empowering Drug Discovery: Applications, Opportunities and Challenges

Qi, Xin, Zhao, Yuanchun, Qi, Zhuang, Hou, Siyu, Chen, Jiajia · 2024 · Molecules · DOI

Full title: Machine Learning Empowering Drug Discovery: Applications, Opportunities and Challenges

Authors: Qi, Xin, Zhao, Yuanchun, Qi, Zhuang, Hou, Siyu, Chen, Jiajia

Year: 2024

Venue: Molecules

DOI: https://doi.org/10.3390/molecules29040903

Paper Fusing Sequence and Structural Knowledge by Heterogeneous Models to Accurately and Interpretively Predict Drug–Target Affinity

Zeng, Xin, Zhong, Kai-Yang, Jiang, Bei, Li, Yi · 2023 · Molecules · DOI

Full title: Fusing Sequence and Structural Knowledge by Heterogeneous Models to Accurately and Interpretively Predict Drug–Target Affinity

Authors: Zeng, Xin, Zhong, Kai-Yang, Jiang, Bei, Li, Yi

Year: 2023

Venue: Molecules

DOI: https://doi.org/10.3390/molecules28248005

Paper The Application of Machine Learning on Antibody Discovery and Optimization

Zheng, Jiayao, Wang, Yu, Qin, Liang, Cui, Lun, Wang, Liqun · 2024 · Molecules · DOI

Full title: The Application of Machine Learning on Antibody Discovery and Optimization

Authors: Zheng, Jiayao, Wang, Yu, Qin, Liang, Cui, Lun, Wang, Liqun

Year: 2024

Venue: Molecules

DOI: https://doi.org/10.3390/molecules29245923

Paper Non-Steroidal Anti-Inflammatory Drugs Are Inhibitors of the Intestinal Proton-Coupled Amino Acid Transporter (PAT1): Ibuprofen and Diclofenac Are Non-Translocated Inhibitors

Nielsen, Carsten Uhd, Jakobsen, Sebastian, Pedersen, Maria L. · 2025 · Pharmaceutics · DOI

Full title: Non-Steroidal Anti-Inflammatory Drugs Are Inhibitors of the Intestinal Proton-Coupled Amino Acid Transporter (PAT1): Ibuprofen and Diclofenac Are Non-Translocated Inhibitors

Authors: Nielsen, Carsten Uhd, Jakobsen, Sebastian, Pedersen, Maria L.

Year: 2025

Venue: Pharmaceutics

DOI: https://doi.org/10.3390/pharmaceutics17010049

Paper Computational Methods in the Design of Anticancer Drugs

Fantacuzzi, Marialuigia, Agamennone, Mariangela · 2024 · Pharmaceuticals · DOI

Full title: Computational Methods in the Design of Anticancer Drugs

Authors: Fantacuzzi, Marialuigia, Agamennone, Mariangela

Year: 2024

Venue: Pharmaceuticals

DOI: https://doi.org/10.3390/ph17040404

Paper Machine Learning and Artificial Intelligence in Therapeutics and Drug Development Life Cycle

Borkotoky, Subhomoi, Joshi, Amit, Kaushik, Vikas, Jha, Anupam Nath · 2022 · IntechOpen eBooks · DOI

Full title: Machine Learning and Artificial Intelligence in Therapeutics and Drug Development Life Cycle

Authors: Borkotoky, Subhomoi, Joshi, Amit, Kaushik, Vikas, Jha, Anupam Nath

Year: 2022

Venue: IntechOpen eBooks

DOI: https://doi.org/10.5772/intechopen.104753

Paper M Protein from Dengue virus oligomerizes to pentameric channel protein: in silico analysis study

Zeba, Ayesha, Sekar, K., Ganjiwale, Anjali · 2023 · Genomics & Informatics · DOI

Full title: M Protein from Dengue virus oligomerizes to pentameric channel protein: in silico analysis study

Authors: Zeba, Ayesha, Sekar, K., Ganjiwale, Anjali

Year: 2023

Venue: Genomics & Informatics

DOI: https://doi.org/10.5808/gi.23035

Paper Drug-Online: an online platform for drug-target interaction, affinity, and binding sites identification using deep learning

Zeng, Xin, Su, Guang-Peng, Li, Shujuan, Lv, Shuang‐Qing, Wen, Meng‐Liang, Li, Yi · 2024 · BMC Bioinformatics · DOI

Full title: Drug-Online: an online platform for drug-target interaction, affinity, and binding sites identification using deep learning

Authors: Zeng, Xin, Su, Guang-Peng, Li, Shujuan, Lv, Shuang‐Qing, Wen, Meng‐Liang, Li, Yi

Year: 2024

Venue: BMC Bioinformatics

DOI: https://doi.org/10.1186/s12859-024-05783-w

Paper Chemoinformatics and artificial intelligence colloquium: progress and challenges in developing bioactive compounds

Bajorath, Jürgen, Chávez‐Hernández, Ana L., Duran‐Frigola, Miquel, Gortari, Eli Fernández‐de, Gasteiger, Johann, López‐López, Edgar, Maggiora, Gerald M., Medina‐Franco, José L., Méndez‐Lucio, Oscar, Mestres, Jordi, Miranda‐Quintana, Ramón Alain, Oprea, Tudor I., Plisson, Fabien, Prieto‐Martínez, Fernando D., Rodríguez-Pérez, Raquel, Rondón-Villarreal, Paola, Saldívar‐González, Fernanda I., Sánchez‐Cruz, Norberto, Valli, Marília · 2022 · Journal of Cheminformatics · DOI

Full title: Chemoinformatics and artificial intelligence colloquium: progress and challenges in developing bioactive compounds

Authors: Bajorath, Jürgen, Chávez‐Hernández, Ana L., Duran‐Frigola, Miquel, Gortari, Eli Fernández‐de, Gasteiger, Johann, López‐López, Edgar, Maggiora, Gerald M., Medina‐Franco, José L., Méndez‐Lucio, Oscar, Mestres, Jordi, Miranda‐Quintana, Ramón Alain, Oprea, Tudor I., Plisson, Fabien, Prieto‐Martínez, Fernando D., Rodríguez-Pérez, Raquel, Rondón-Villarreal, Paola, Saldívar‐González, Fernanda I., Sánchez‐Cruz, Norberto, Valli, Marília

Year: 2022

Venue: Journal of Cheminformatics

DOI: https://doi.org/10.1186/s13321-022-00661-0

Paper Single-cell profiling of SLC family transporters: uncovering the role of SLC7A1 in osteosarcoma

Liao, Yan, Chen, Junkai, Yao, Hao, Zheng, Ting, Tu, Jian, Chen, Wei‐Dong, Guo, Zhen, Zou, Yutong, Wen, Lili, Xie, X. Sunney · 2025 · Journal of Translational Medicine · DOI

Full title: Single-cell profiling of SLC family transporters: uncovering the role of SLC7A1 in osteosarcoma

Authors: Liao, Yan, Chen, Junkai, Yao, Hao, Zheng, Ting, Tu, Jian, Chen, Wei‐Dong, Guo, Zhen, Zou, Yutong, Wen, Lili, Xie, X. Sunney

Year: 2025

Venue: Journal of Translational Medicine

DOI: https://doi.org/10.1186/s12967-025-06086-1

Paper Benchmarking AlphaFold ‐enabled molecular docking predictions for antibiotic discovery

Wong, Felix, Krishnan, Aarti, Zheng, Erica J., Stärk, H., Manson, Abigail L., Earl, Ashlee M., Jaakkola, Tommi, Collins, James J. · 2022 · Molecular Systems Biology · DOI

Full title: Benchmarking AlphaFold ‐enabled molecular docking predictions for antibiotic discovery

Authors: Wong, Felix, Krishnan, Aarti, Zheng, Erica J., Stärk, H., Manson, Abigail L., Earl, Ashlee M., Jaakkola, Tommi, Collins, James J.

Year: 2022

Venue: Molecular Systems Biology

DOI: https://doi.org/10.15252/msb.202211081

Paper Exploring the ability of machine learning-based virtual screening models to identify the functional groups responsible for binding

Hadfield, Thomas E., Scantlebury, Jack, Deane, Charlotte M. · 2023 · Journal of Cheminformatics · DOI

Full title: Exploring the ability of machine learning-based virtual screening models to identify the functional groups responsible for binding

Authors: Hadfield, Thomas E., Scantlebury, Jack, Deane, Charlotte M.

Year: 2023

Venue: Journal of Cheminformatics

DOI: https://doi.org/10.1186/s13321-023-00755-3

Paper Accurate Pocket Identification for Binding-Site-Agnostic Docking

Balytskyi, Yaroslav, Hubenko, Inna, Balytska, Alina, Kelly, Christopher V. · 2025 · Preprints.org · DOI

Full title: Accurate Pocket Identification for Binding-Site-Agnostic Docking

Authors: Balytskyi, Yaroslav, Hubenko, Inna, Balytska, Alina, Kelly, Christopher V.

Year: 2025

Venue: Preprints.org

DOI: https://doi.org/10.20944/preprints202502.0352.v2

Paper Fusing Sequence and Structural Knowledge by Heterogeneous Models to Accurately and Interpretively Predict Drug-Target Affinity

Zeng, Xin, Zhong, Kai-Yang, Jiang, Bei, Li, Yi · 2023 · Preprints.org · DOI

Full title: Fusing Sequence and Structural Knowledge by Heterogeneous Models to Accurately and Interpretively Predict Drug-Target Affinity

Authors: Zeng, Xin, Zhong, Kai-Yang, Jiang, Bei, Li, Yi

Year: 2023

Venue: Preprints.org

DOI: https://doi.org/10.20944/preprints202310.1539.v1

Paper FusionPDB: a unique knowledgebase of human fusion proteins of consistent annotation across genome/ transcript/ protein/ interaction levels

Kumar, Himansu, Tang, Lin-Ya, Yang, Chengyuan, Kim, Pora · 2022 · DOI

Full title: FusionPDB: a unique knowledgebase of human fusion proteins of consistent annotation across genome/ transcript/ protein/ interaction levels

Authors: Kumar, Himansu, Tang, Lin-Ya, Yang, Chengyuan, Kim, Pora

Year: 2022

DOI: https://doi.org/10.21203/rs.3.rs-2202839/v1

Paper Multimodal Protein Representation Learning and Target-aware Variational Auto-encoders for Protein-binding Ligand Generation

Ngo, Nhat Khang, Hy, Truong Son · 2023 · Research Square (Research Square) · DOI

Full title: Multimodal Protein Representation Learning and Target-aware Variational Auto-encoders for Protein-binding Ligand Generation

Authors: Ngo, Nhat Khang, Hy, Truong Son

Year: 2023

Venue: Research Square (Research Square)

DOI: https://doi.org/10.21203/rs.3.rs-3504792/v1

Paper Lira: Rotational Invariant Shape and Electrostatic Descriptors for Small Molecules and Protein Pockets based on Real Spherical Harmonics

Caires, Fernando R., Silva, Samuel Reghim, Veríssimo-Alves, Marcos, Pinheiro, Vitor B., Montalvão, Rinaldo W. · 2022 · DOI

Full title: Lira: Rotational Invariant Shape and Electrostatic Descriptors for Small Molecules and Protein Pockets based on Real Spherical Harmonics

Authors: Caires, Fernando R., Silva, Samuel Reghim, Veríssimo-Alves, Marcos, Pinheiro, Vitor B., Montalvão, Rinaldo W.

Year: 2022

DOI: https://doi.org/10.1101/2022.01.19.476747

Paper Fragment-Based Ligand Generation Guided By Geometric Deep Learning On Protein-Ligand Structure

Powers, Alexander S., Yu, Helen H., Suriana, Patricia, Dror, Ron O. · 2022 · DOI

Full title: Fragment-Based Ligand Generation Guided By Geometric Deep Learning On Protein-Ligand Structure

Authors: Powers, Alexander S., Yu, Helen H., Suriana, Patricia, Dror, Ron O.

Year: 2022

DOI: https://doi.org/10.1101/2022.03.17.484653

Paper A chronopharmacology-friendly multi-target therapeutics based on AI: the example of therapeutic hypothermia

Liu, Fei, Jiang, Xiangkang, Zhang, Mao · 2022 · DOI

Full title: A chronopharmacology-friendly multi-target therapeutics based on AI: the example of therapeutic hypothermia

Authors: Liu, Fei, Jiang, Xiangkang, Zhang, Mao

Year: 2022

DOI: https://doi.org/10.1101/2022.03.07.22271997

Paper Investigating the folding dynamics of NS2B protein of Zika virus

Kumar, Ankur, Kumar, Prateek, Mishra, Pushpendra Mani, Giri, Rajanish · 2022 · DOI

Full title: Investigating the folding dynamics of NS2B protein of Zika virus

Authors: Kumar, Ankur, Kumar, Prateek, Mishra, Pushpendra Mani, Giri, Rajanish

Year: 2022

DOI: https://doi.org/10.1101/2022.12.12.520106

Paper Exploring The Ability Of Machine Learning-Based Virtual Screening Models To Identify The Functional Groups Responsible For Binding

Hadfield, Thomas E., Scantlebury, Jack, Deane, Charlotte M. · 2023 · DOI

Full title: Exploring The Ability Of Machine Learning-Based Virtual Screening Models To Identify The Functional Groups Responsible For Binding

Authors: Hadfield, Thomas E., Scantlebury, Jack, Deane, Charlotte M.

Year: 2023

DOI: https://doi.org/10.1101/2023.04.29.538820

Paper Protein property prediction based on local environment by 3D equivariant convolutional neural networks

Chen, He, Cheng, Yifan, Dong, Jianqiang, Mao, Jie, Wang, Xin, Gao, Yuan, Li, Yuchao, Wang, Chengzhi, Wu, Qiong · 2024 · DOI

Full title: Protein property prediction based on local environment by 3D equivariant convolutional neural networks

Authors: Chen, He, Cheng, Yifan, Dong, Jianqiang, Mao, Jie, Wang, Xin, Gao, Yuan, Li, Yuchao, Wang, Chengzhi, Wu, Qiong

Year: 2024

DOI: https://doi.org/10.1101/2024.02.07.579261

Paper NRGRank: Coarse-grained structurally-informed ultra-massive virtual screening

DesCôteaux, Thomas, Najmanovich, Rafaël, Najmanovich, Rafael · 2025 · DOI

Full title: NRGRank: Coarse-grained structurally-informed ultra-massive virtual screening

Authors: DesCôteaux, Thomas, Najmanovich, Rafaël, Najmanovich, Rafael

Year: 2025

DOI: https://doi.org/10.1101/2025.02.17.638675

Paper Highly accurate protein structure prediction-based virtual docking pipeline accelerating the identification of anti-schistosomal compounds

Cheng, Wenjun, Gu, Mengjie, Wang, Yuepeng, Wang, Jing, Li, Shan, Chen, Gongwen, Chen, Xu, Oyeyemi, Oyetunde T., Hong, Yang, Hu, Wei, Wang, Jipeng · 2025 · DOI

Full title: Highly accurate protein structure prediction-based virtual docking pipeline accelerating the identification of anti-schistosomal compounds

Authors: Cheng, Wenjun, Gu, Mengjie, Wang, Yuepeng, Wang, Jing, Li, Shan, Chen, Gongwen, Chen, Xu, Oyeyemi, Oyetunde T., Hong, Yang, Hu, Wei, Wang, Jipeng

Year: 2025

DOI: https://doi.org/10.1101/2025.06.09.658570

Paper Attention-based approach to predict drug-target interactions across seven target superfamilies

Schulman, Aron, Rousu, Juho, Aittokallio, Tero, Tanoli, Ziaurrehman · 2024 · DOI

Full title: Attention-based approach to predict drug-target interactions across seven target superfamilies

Authors: Schulman, Aron, Rousu, Juho, Aittokallio, Tero, Tanoli, Ziaurrehman

Year: 2024

DOI: https://doi.org/10.1101/2024.03.20.585893

Paper Structure and dynamics of pteridine reductase 1: the key phenomena relevant to enzyme function and drug design

Panecka-Hofman, Joanna, Poehner, Ina · 2023 · European Biophysics Journal · DOI

Full title: Structure and dynamics of pteridine reductase 1: the key phenomena relevant to enzyme function and drug design

Authors: Panecka-Hofman, Joanna, Poehner, Ina

Year: 2023

Venue: European Biophysics Journal

DOI: https://doi.org/10.1007/s00249-023-01677-6

Paper Sequence-based drug design as a concept in computational drug design

Chen, Lifan, Fan, Zisheng, Chang, Jie, Yang, Ruirui, Hou, Hui, Guo, Hao, Zhang, Yinghui, Yang, Tianbiao, Zhou, Chenmao, Sui, Qibang, Chen, Zhengyang, Chen, Zheng, Hao, Xinyue, Zhang, Keke, Cui, Rongrong, Zhang, Zehong, Ma, Hudson, Ding, Yiluan, Zhang, Naixia, Lu, Xiaojie, Luo, Xiaomin, Jiang, Hualiang, Zhang, Sulin, Zheng, Mingyue · 2023 · Nature Communications · DOI

Full title: Sequence-based drug design as a concept in computational drug design

Authors: Chen, Lifan, Fan, Zisheng, Chang, Jie, Yang, Ruirui, Hou, Hui, Guo, Hao, Zhang, Yinghui, Yang, Tianbiao, Zhou, Chenmao, Sui, Qibang, Chen, Zhengyang, Chen, Zheng, Hao, Xinyue, Zhang, Keke, Cui, Rongrong, Zhang, Zehong, Ma, Hudson, Ding, Yiluan, Zhang, Naixia, Lu, Xiaojie, Luo, Xiaomin, Jiang, Hualiang, Zhang, Sulin, Zheng, Mingyue

Year: 2023

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-023-39856-w

Paper A multi-targeted computational drug discovery approach for repurposing tetracyclines against monkeypox virus

Alandijany, Thamir A., El-Daly, Mai M., Tolah, Ahmed M., Bajrai, Leena H., Khateb, Aiah M., Kumar, Geethu S, Dubey, Amit, Dwivedi, Vivek Dhar, Azhar, Esam I. · 2023 · Scientific Reports · DOI

Full title: A multi-targeted computational drug discovery approach for repurposing tetracyclines against monkeypox virus

Authors: Alandijany, Thamir A., El-Daly, Mai M., Tolah, Ahmed M., Bajrai, Leena H., Khateb, Aiah M., Kumar, Geethu S, Dubey, Amit, Dwivedi, Vivek Dhar, Azhar, Esam I.

Year: 2023

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-023-41820-z

Paper Identification of potential modulators of IFITM3 by in-silico modeling and virtual screening

Tiwari, Vikas, Viswanath, Shruthi · 2022 · Scientific Reports · DOI

Full title: Identification of potential modulators of IFITM3 by in-silico modeling and virtual screening

Authors: Tiwari, Vikas, Viswanath, Shruthi

Year: 2022

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-022-20259-8

Paper Bioinformatics approach for discovery of potential lead compound of NSP6 of SARS-CoV-2 using structure based virtual screening and molecular dynamics simulations.

Salama, Mohammed M, Shafaa, Medhat W, El-Nagdy, Mohamed E, Hasan, Mohamed E · 2025 · Scientific reports · DOI

Full title: Bioinformatics approach for discovery of potential lead compound of NSP6 of SARS-CoV-2 using structure based virtual screening and molecular dynamics simulations.

Authors: Salama, Mohammed M, Shafaa, Medhat W, El-Nagdy, Mohamed E, Hasan, Mohamed E

Year: 2025

Venue: Scientific reports

DOI: https://doi.org/10.1038/s41598-025-22409-0

Paper Computing the relative binding affinity of ligands based on a pairwise binding comparison network

Yu, Jie, Li, Zhaojun, Chen, Geng, Kong, Xiangtai, Hu, Jie, Wang, Dingyan, Cao, Duanhua, Li, Yanbei, Huo, Ruifeng, Wang, Gang, Liu, Xiaohong, Jiang, Hualiang, Li, Xutong, Luo, Xiaomin, Zheng, Mingyue · 2023 · Nature Computational Science · DOI

Full title: Computing the relative binding affinity of ligands based on a pairwise binding comparison network

Authors: Yu, Jie, Li, Zhaojun, Chen, Geng, Kong, Xiangtai, Hu, Jie, Wang, Dingyan, Cao, Duanhua, Li, Yanbei, Huo, Ruifeng, Wang, Gang, Liu, Xiaohong, Jiang, Hualiang, Li, Xutong, Luo, Xiaomin, Zheng, Mingyue

Year: 2023

Venue: Nature Computational Science

DOI: https://doi.org/10.1038/s43588-023-00529-9

Paper Specialty grand challenges in theoretical modeling, structure prediction and design

Exertier, Cécile, Ilari, Andrea · 2025 · Frontiers in Chemical Biology · DOI

Full title: Specialty grand challenges in theoretical modeling, structure prediction and design

Authors: Exertier, Cécile, Ilari, Andrea

Year: 2025

Venue: Frontiers in Chemical Biology

DOI: https://doi.org/10.3389/fchbi.2025.1635423

Paper Towards rational computational peptide design

Chang, Liwei, Mondal, Arup, Pérez, Alberto · 2022 · Frontiers in Bioinformatics · DOI

Full title: Towards rational computational peptide design

Authors: Chang, Liwei, Mondal, Arup, Pérez, Alberto

Year: 2022

Venue: Frontiers in Bioinformatics

DOI: https://doi.org/10.3389/fbinf.2022.1046493

Paper Target-driven machine learning-enabled virtual screening (TAME-VS) platform for early-stage hit identification

Bian, Yuemin, Kwon, Jason J., Liu, Cong, Margiotta, Enrico, Shekhar, Mrinal, Gould, Alexandra E. · 2023 · Frontiers in Molecular Biosciences · DOI

Full title: Target-driven machine learning-enabled virtual screening (TAME-VS) platform for early-stage hit identification

Authors: Bian, Yuemin, Kwon, Jason J., Liu, Cong, Margiotta, Enrico, Shekhar, Mrinal, Gould, Alexandra E.

Year: 2023

Venue: Frontiers in Molecular Biosciences

DOI: https://doi.org/10.3389/fmolb.2023.1163536

Paper Editorial: Structural studies of bacteria and viruses

Pastore, Annalisa · 2025 · Frontiers in Molecular Biosciences · DOI

Full title: Editorial: Structural studies of bacteria and viruses

Authors: Pastore, Annalisa

Year: 2025

Venue: Frontiers in Molecular Biosciences

DOI: https://doi.org/10.3389/fmolb.2025.1605596

Paper Potential Inhibitors of Lumpy Skin Disease’s Viral Protein (DNA Polymerase): A Combination of Bioinformatics Approaches

Zia, S. H., Sumon, Mahmudul Reza, Ashik, Md-Ashiqur, Basar, Abul, Lim, Sang Jin, Oh, Yeonsu, Park, Yung Chul, Rahman, Md. Mafizur · 2024 · Animals · DOI

Full title: Potential Inhibitors of Lumpy Skin Disease’s Viral Protein (DNA Polymerase): A Combination of Bioinformatics Approaches

Authors: Zia, S. H., Sumon, Mahmudul Reza, Ashik, Md-Ashiqur, Basar, Abul, Lim, Sang Jin, Oh, Yeonsu, Park, Yung Chul, Rahman, Md. Mafizur

Year: 2024

Venue: Animals

DOI: https://doi.org/10.3390/ani14091283

Paper From Code to Cure: The Impact of Artificial Intelligence in Biomedical Applications

Gromiha, M. Michael, Preethi, P., Pandey, Medha · 2024 · BioMedInformatics · DOI

Full title: From Code to Cure: The Impact of Artificial Intelligence in Biomedical Applications

Authors: Gromiha, M. Michael, Preethi, P., Pandey, Medha

Year: 2024

Venue: BioMedInformatics

DOI: https://doi.org/10.3390/biomedinformatics4010030

Paper Artificial Intelligence in Clinical Medicine: Challenges Across Diagnostic Imaging, Clinical Decision Support, Surgery, Pathology, and Drug Discovery

Öğüt, Eren · 2025 · Clinics and Practice · DOI

Full title: Artificial Intelligence in Clinical Medicine: Challenges Across Diagnostic Imaging, Clinical Decision Support, Surgery, Pathology, and Drug Discovery

Authors: Öğüt, Eren

Year: 2025

Venue: Clinics and Practice

DOI: https://doi.org/10.3390/clinpract15090169

Paper Trends and Applications in Computationally Driven Drug Repurposing

Pinzi, Luca, Rastelli, Giulio · 2023 · International Journal of Molecular Sciences · DOI

Full title: Trends and Applications in Computationally Driven Drug Repurposing

Authors: Pinzi, Luca, Rastelli, Giulio

Year: 2023

Venue: International Journal of Molecular Sciences

DOI: https://doi.org/10.3390/ijms242216511

Paper A divide and conquer approach (DACA) to predict high fidelity structure of large multidomain protein BRWD1

Mondal, Rajkrishna; Mandal, Malay; Lahiri, Tapobrata · 2023 · DOI

Full title: A divide and conquer approach (DACA) to predict high fidelity structure of large multidomain protein BRWD1

Authors: Mondal, Rajkrishna; Mandal, Malay; Lahiri, Tapobrata

Year: 2023

DOI: https://doi.org/10.1101/2023.07.10.548240

Paper Hybrid protein-ligand binding residue prediction with protein language models: Does the structure matter?

Gamouh, Hamza; Novotný, Marián; Hoksza, David · 2023 · DOI

Full title: Hybrid protein-ligand binding residue prediction with protein language models: Does the structure matter?

Authors: Gamouh, Hamza; Novotný, Marián; Hoksza, David

Year: 2023

DOI: https://doi.org/10.1101/2023.08.11.553028

Paper AF2BIND: Predicting ligand-binding sites using the pair representation of AlphaFold2

Gazizov, Artem; Lian, Anna; Goverde, Casper A. et al. · 2023 · DOI

Full title: AF2BIND: Predicting ligand-binding sites using the pair representation of AlphaFold2

Authors: Gazizov, Artem; Lian, Anna; Goverde, Casper A.; Ovchinnikov, Sergey; Polizzi, Nicholas F.

Year: 2023

DOI: https://doi.org/10.1101/2023.10.15.562410

Paper Structural Insights into Dopamine Receptor-Ligand Interactions: From Agonists to Antagonists

Barbosa, Emmanuel Duarte; Clift, Heather E.; Olson, Linda J. et al. · 2023 · DOI

Full title: Structural Insights into Dopamine Receptor-Ligand Interactions: From Agonists to Antagonists

Authors: Barbosa, Emmanuel Duarte; Clift, Heather E.; Olson, Linda J.; Zhu, Lan; Liu, Wei

Year: 2023

DOI: https://doi.org/10.1101/2023.11.03.565579

Paper Targeting transcription factors through an IMiD independent zinc finger domain

Liu, Bee Hui; Liu, Miao; Sridhar, R. et al. · 2024 · DOI

Full title: Targeting transcription factors through an IMiD independent zinc finger domain

Authors: Liu, Bee Hui; Liu, Miao; Sridhar, R.; Jaladanki, Chaitanya K.; Gao, Chong; Tang, Jing; Kumari, Kalpana; Go, Mei‐Lin; Vu, Kim Anh L.; Seo, Hyuk‐Soo; Song, Kijun; Tian, Xi; Li, Feng; Tan, Justin L.; Bassal, Mahmoud A.; Arthanari, Haribabu; Qi, Jun; Dhe‐Paganon, Sirano; Fan, Hao; Tenen, Daniel G.; Chai, Li

Year: 2024

DOI: https://doi.org/10.1101/2024.01.03.574032

Paper NeuroFold: A Multimodal Approach to Generating Novel Protein Variants in silico

Amani, Keaun; Fish, Michael; Smith, Matthew D. et al. · 2024 · DOI

Full title: NeuroFold: A Multimodal Approach to Generating Novel Protein Variants in silico

Authors: Amani, Keaun; Fish, Michael; Smith, Matthew D.; Castroverde, Christian Danve M.

Year: 2024

DOI: https://doi.org/10.1101/2024.03.12.584504

Paper A Folding-Docking-Affinity framework for protein-ligand binding affinity prediction

Wu, Ming-Hsiu; Xie, Ziqian; Zhi, Degui · 2025 · Communications Chemistry · DOI

Full title: A Folding-Docking-Affinity framework for protein-ligand binding affinity prediction

Authors: Wu, Ming-Hsiu; Xie, Ziqian; Zhi, Degui

Year: 2025

Venue: Communications Chemistry

DOI: https://doi.org/10.1038/s42004-025-01506-1

Paper Complex-based Ligand-Binding Proteins Redesign by Equivariant Diffusion-based Generative Models

Nguyen, Viet Thanh Duy; Nguyen, Nhan Duc; Hy, Truong Son · 2024 · DOI

Full title: Complex-based Ligand-Binding Proteins Redesign by Equivariant Diffusion-based Generative Models

Authors: Nguyen, Viet Thanh Duy; Nguyen, Nhan Duc; Hy, Truong Son

Year: 2024

DOI: https://doi.org/10.1101/2024.04.17.589997

Paper Exploring Protein Patterns, Cavity Interactions, and Therapeutic Insights in Cancer

Nevado, Paloma Tejera; Otero-Carrasco, Belén; Rodríguez‐González, Alejandro · 2025 · DOI

Full title: Exploring Protein Patterns, Cavity Interactions, and Therapeutic Insights in Cancer

Authors: Nevado, Paloma Tejera; Otero-Carrasco, Belén; Rodríguez‐González, Alejandro

Year: 2025

DOI: https://doi.org/10.1101/2025.06.03.657615

Paper A potential implication of UDP-glucuronosyltransferase 2B10 in the detoxification of drugs used in pediatric hematopoietic stem cell transplantation setting: an in silico investigation

Robin, Shannon; Hassine, Khalil Ben; Muthukumaran, Jayaraman et al. · 2022 · BMC Molecular and Cell Biology · DOI

Full title: A potential implication of UDP-glucuronosyltransferase 2B10 in the detoxification of drugs used in pediatric hematopoietic stem cell transplantation setting: an in silico investigation

Authors: Robin, Shannon; Hassine, Khalil Ben; Muthukumaran, Jayaraman; Mlakar, Simona Jurković; Krajinović, Maja; Nava, Tiago; Uppugunduri, Chakradhara Rao S.; Ansari, Marc

Year: 2022

Venue: BMC Molecular and Cell Biology

DOI: https://doi.org/10.1186/s12860-021-00402-5

Paper Sequence-based drug-target affinity prediction using weighted graph neural networks

Jiang, Mingjian; Wang, Shuang; Zhang, Shugang et al. · 2022 · BMC Genomics · DOI

Full title: Sequence-based drug-target affinity prediction using weighted graph neural networks

Authors: Jiang, Mingjian; Wang, Shuang; Zhang, Shugang; Zhou, Wei; Zhang, Yuanyuan; Li, Zhen

Year: 2022

Venue: BMC Genomics

DOI: https://doi.org/10.1186/s12864-022-08648-9

Paper From byte to bench to bedside: molecular dynamics simulations and drug discovery

Ahmed, M.W.; Maldonado, Alex M.; Durrant, Jacob D. · 2023 · BMC Biology · DOI

Full title: From byte to bench to bedside: molecular dynamics simulations and drug discovery

Authors: Ahmed, M.W.; Maldonado, Alex M.; Durrant, Jacob D.

Year: 2023

Venue: BMC Biology

DOI: https://doi.org/10.1186/s12915-023-01791-z

Paper Molecular mechanism of interaction between fatty acid delta 6 desaturase and acyl-CoA by computational prediction

Cui, Jie; Chen, Haiqin; Tang, Xin et al. · 2022 · AMB Express · DOI

Full title: Molecular mechanism of interaction between fatty acid delta 6 desaturase and acyl-CoA by computational prediction

Authors: Cui, Jie; Chen, Haiqin; Tang, Xin; Zhang, Hao; Chen, Yong Q.; Chen, Wei

Year: 2022

Venue: AMB Express

DOI: https://doi.org/10.1186/s13568-022-01410-0

Paper Hypothetical protein CuvA (Rv1422) from Mycobacterium tuberculosis H37Rv interacts with uridine diphosphate N-acetylglucosamine as a key precursor of cell wall

Jeong, Yoon Chae; Park, Jihyun; Cheon, Yu Jeong et al. · 2023 · Applied Biological Chemistry · DOI

Full title: Hypothetical protein CuvA (Rv1422) from Mycobacterium tuberculosis H37Rv interacts with uridine diphosphate N-acetylglucosamine as a key precursor of cell wall

Authors: Jeong, Yoon Chae; Park, Jihyun; Cheon, Yu Jeong; Lee, Ki Seog

Year: 2023

Venue: Applied Biological Chemistry

DOI: https://doi.org/10.1186/s13765-023-00840-z

Paper A predicted structure of NADPH Oxidase 1 identifies key components of ROS generation and strategies for inhibition

Liu, Yezhou; Liang, Shiyu; Shi, Danfeng et al. · 2023 · PLoS ONE · DOI

Full title: A predicted structure of NADPH Oxidase 1 identifies key components of ROS generation and strategies for inhibition

Authors: Liu, Yezhou; Liang, Shiyu; Shi, Danfeng; Zhang, Yue; Bai, Chen; Ye, Richard D.

Year: 2023

Venue: PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0285206

Paper Towards a General Intermolecular Binding Affinity Calculator

Li, Wei · 2022 · Preprints.org · DOI

Full title: Towards a General Intermolecular Binding Affinity Calculator

Authors: Li, Wei

Year: 2022

Venue: Preprints.org

DOI: https://doi.org/10.20944/preprints202208.0213.v1

Paper A Folding-Docking-Affinity framework for protein-ligand binding affinity prediction

Wu, Ming-Hsiu; Xie, Ziqian; Zhi, Degui · 2025 · Communications Chemistry · DOI

Full title: A Folding-Docking-Affinity framework for protein-ligand binding affinity prediction

Authors: Wu, Ming-Hsiu; Xie, Ziqian; Zhi, Degui

Year: 2025

Venue: Communications Chemistry

DOI: https://doi.org/10.1038/s42004-025-01506-1

Paper AI based natural inhibitor targeting RPS20 for colorectal cancer treatment using integrated computational approaches

Nouman Ali; Roman Akbar; Amna Saleem et al. · 2025 · Scientific Reports · DOI

Full title: AI based natural inhibitor targeting RPS20 for colorectal cancer treatment using integrated computational approaches

Authors: Nouman Ali; Roman Akbar; Amna Saleem; Adeeba Ali; Aamir Ali

Year: 2025

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-025-07574-6

Paper AlphaFold accelerates artificial intelligence powered drug discovery: efficient discovery of a novel CDK20 small molecule inhibitor

Ren, Feng; Ding, Xiao; Zheng, Min et al. · 2023 · Chemical Science · DOI

Full title: AlphaFold accelerates artificial intelligence powered drug discovery: efficient discovery of a novel CDK20 small molecule inhibitor

Authors: Ren, Feng; Ding, Xiao; Zheng, Min; Korzinkin, Mikhail; Cai, Xin; Zhu, Wei; Mantsyzov, Alexey B.; Aliper, Alex; Aladinskiy, Vladimir; Cao, Zhongying; Kong, Shanshan; Long, Xi; Liu, Bonnie Hei Man; Liu, Yingtao; Naumov, Vladimir; Shneyderman, Anastasia; Ozerov, Ivan V.; Wang, Ju; Pun, Frank W.; Polykovskiy, Daniil; Sun, Chong; Levitt, Michael D.; Aspuru‐Guzik, Alán; Zhavoronkov, Alex

Year: 2023

Venue: Chemical Science

DOI: https://doi.org/10.1039/d2sc05709c

Paper Exploring the selectivity of cytochrome P450 for enhanced novel anticancer agent synthesis

Čivić, Janko; McFarlane, Neil R.; Masschelein, Joleen et al. · 2024 · Faraday Discussions · DOI

Full title: Exploring the selectivity of cytochrome P450 for enhanced novel anticancer agent synthesis

Authors: Čivić, Janko; McFarlane, Neil R.; Masschelein, Joleen; Harvey, Jeremy N.

Year: 2024

Venue: Faraday Discussions

DOI: https://doi.org/10.1039/d4fd00004h

Paper Generating 3D molecules conditional on receptor binding sites with deep generative models

Ragoza, Matthew; Masuda, Tomohide; Koes, David Ryan · 2022 · Chemical Science · DOI

Full title: Generating 3D molecules conditional on receptor binding sites with deep generative models

Authors: Ragoza, Matthew; Masuda, Tomohide; Koes, David Ryan

Year: 2022

Venue: Chemical Science

DOI: https://doi.org/10.1039/d1sc05976a

Paper Identification of binding interaction between Curcumin derivative and PERK13 Proline rich receptor like protein kinase protein using In silico docking techniques – to help plants tackle salt water

Vaithyanathan, Prakash · 2021 · DOI

Full title: Identification of binding interaction between Curcumin derivative and PERK13 Proline rich receptor like protein kinase protein using In silico docking techniques – to help plants tackle salt water

Authors: Vaithyanathan, Prakash

Year: 2021

DOI: https://doi.org/10.1101/2021.10.15.464501

Paper AlphaFold2 transmembrane protein structure prediction shines

Hegedűs, Tamás; Geisler, Markus; Lukács, Gergely L. et al. · 2021 · DOI

Full title: AlphaFold2 transmembrane protein structure prediction shines

Authors: Hegedűs, Tamás; Geisler, Markus; Lukács, Gergely L.; Farkas, Bianka

Year: 2021

DOI: https://doi.org/10.1101/2021.08.21.457196

Paper Flavobacterium johnsoniae Tyrosine Ammonia Lyase (FjTAL) in-silico Structure Prediction and Molecular Docking to L-Tyrosine, p-Coumaric Acid (pHCA) and Caffeic Acid

Majd, Seyyed Amirreza Mousavi · 2022 · DOI

Full title: Flavobacterium johnsoniae Tyrosine Ammonia Lyase (FjTAL) in-silico Structure Prediction and Molecular Docking to L-Tyrosine, p-Coumaric Acid (pHCA) and Caffeic Acid

Authors: Majd, Seyyed Amirreza Mousavi

Year: 2022

DOI: https://doi.org/10.1101/2022.02.09.479702

Paper CavitySpace: A database of potential ligand binding sites in the human proteome

Wang, Shiwei; Lin, Haoyu; Huang, Zhixian et al. · 2022 · DOI

Full title: CavitySpace: A database of potential ligand binding sites in the human proteome

Authors: Wang, Shiwei; Lin, Haoyu; Huang, Zhixian; He, Yufeng; Deng, Xiaobing; Xu, Youjun; Pei, Jianfeng; Lai, Luhua

Year: 2022

DOI: https://doi.org/10.1101/2022.01.25.477691

Paper Predicting the locations of cryptic pockets from single protein structures using the PocketMiner graph neural network

Meller, Artur; Ward, Michael D.; Borowsky, Jonathan et al. · 2022 · DOI

Full title: Predicting the locations of cryptic pockets from single protein structures using the PocketMiner graph neural network

Authors: Meller, Artur; Ward, Michael D.; Borowsky, Jonathan; Lotthammer, Jeffrey M.; Kshirsagar, Meghana; Oviedo, Felipe; Ferres, Juan Lavista; Bowman, Gregory R.

Year: 2022

DOI: https://doi.org/10.1101/2022.06.28.497399

Paper Structural Modeling of Peptide Toxin - Ion Channel Interactions using RosettaDock

Mateos, Diego López; Yarov‐Yarovoy, Vladimir · 2022 · DOI

Full title: Structural Modeling of Peptide Toxin - Ion Channel Interactions using RosettaDock

Authors: Mateos, Diego López; Yarov‐Yarovoy, Vladimir

Year: 2022

DOI: https://doi.org/10.1101/2022.06.29.498146

Paper xTrimoDock: Rigid Protein Docking via Cross-Modal Representation Learning and Spectral Algorithm

Luo, Yujie; Li, Shaochuan; Sun, Yiwu et al. · 2023 · DOI

Full title: xTrimoDock: Rigid Protein Docking via Cross-Modal Representation Learning and Spectral Algorithm

Authors: Luo, Yujie; Li, Shaochuan; Sun, Yiwu; Wang, Ruijia; Tang, Tingting; Hongdu, Beiqi; Cheng, Xingyi; Shi, Chuan; Li, Hui; Song, Le

Year: 2023

DOI: https://doi.org/10.1101/2023.02.06.527251

Paper Comprehensive Approach to Simulating Large Scale Conformational Changes in Biological Systems Utilizing a Path Collective Variable and New Barrier Restraint

Kolossváry, István; Sherman, Woody · 2023 · DOI

Full title: Comprehensive Approach to Simulating Large Scale Conformational Changes in Biological Systems Utilizing a Path Collective Variable and New Barrier Restraint

Authors: Kolossváry, István; Sherman, Woody

Year: 2023

DOI: https://doi.org/10.1101/2023.03.26.534298

Paper Reconstruction of TrkB complex assemblies and localizing antidepressant targets using Artificial Intelligence

Xiang, Xufu; Qian, Chungen; Yao, Hanbo et al. · 2023 · DOI

Full title: Reconstruction of TrkB complex assemblies and localizing antidepressant targets using Artificial Intelligence

Authors: Xiang, Xufu; Qian, Chungen; Yao, Hanbo; Li, Pengjie; Cheng, Bangning; Wei, Daoshun; An, Wenjun; Lu, Yuming; Chu, Ming; Wei, Lanlan; Liu, Bi‐Feng; Junfa, Xu; Liu, Xin; Xia, Fuzhen

Year: 2023

DOI: https://doi.org/10.1101/2023.02.21.529454

Paper Fast, accurate ranking of engineered proteins by receptor binding propensity using structure modeling

Ding, Xiaozhe; Chen, Xinhong; Sullivan, Erin E. et al. · 2023 · DOI

Full title: Fast, accurate ranking of engineered proteins by receptor binding propensity using structure modeling

Authors: Ding, Xiaozhe; Chen, Xinhong; Sullivan, Erin E.; Shay, Timothy F.; Gradinaru, Viviana

Year: 2023

DOI: https://doi.org/10.1101/2023.01.11.523680

Paper Structure-Based Neural Network Protein-Carbohydrate Interaction Predictions at the Residue Level

Canner, Samuel W.; Shanker, Sudhanshu; Gray, Jeffrey J. · 2023 · DOI

Full title: Structure-Based Neural Network Protein-Carbohydrate Interaction Predictions at the Residue Level

Authors: Canner, Samuel W.; Shanker, Sudhanshu; Gray, Jeffrey J.

Year: 2023

DOI: https://doi.org/10.1101/2023.03.14.531382

Paper Guiding discovery of protein sequence-structure-function modeling

Hussain, Azam; Brooks, Charles L. · 2024 · Bioinformatics · DOI

Full title: Guiding discovery of protein sequence-structure-function modeling

Authors: Hussain, Azam; Brooks, Charles L.

Year: 2024

Venue: Bioinformatics

DOI: https://doi.org/10.1093/bioinformatics/btae002

Paper Understanding ATP binding to DosS catalytic domain with a short ATP-lid

Larson, Grant; Windsor, Peter; Smithwick, Elizabeth M. et al. · 2023 · DOI

Full title: Understanding ATP binding to DosS catalytic domain with a short ATP-lid

Authors: Larson, Grant; Windsor, Peter; Smithwick, Elizabeth M.; Shi, Ke; Aihara, Hideki; Damodaran, Anoop R.; Bhagi‐Damodaran, Ambika

Year: 2023

DOI: https://doi.org/10.1101/2023.05.29.542785

Paper Data-Driven Modeling and Analysis of Fatty Acid Desaturase in Plants

McNaughton, Andrew; Shanklin, John; Raugei, Simone et al. · 2023 · DOI

Full title: Data-Driven Modeling and Analysis of Fatty Acid Desaturase in Plants

Authors: McNaughton, Andrew; Shanklin, John; Raugei, Simone; Kumar, Neeraj

Year: 2023

DOI: https://doi.org/10.1101/2023.08.17.553759

Paper HTLV-1 reverse transcriptase homology model provides structural basis for sensitivity to existing nucleoside/nucleotide reverse transcriptase inhibitors

Tardiota, Nicolas; Jaberolansar, Noushin; Lackenby, Julia et al. · 2023 · DOI

Full title: HTLV-1 reverse transcriptase homology model provides structural basis for sensitivity to existing nucleoside/nucleotide reverse transcriptase inhibitors

Authors: Tardiota, Nicolas; Jaberolansar, Noushin; Lackenby, Julia; Chappell, Keith J.; O’Donnell, Jake S.

Year: 2023

DOI: https://doi.org/10.1101/2023.05.25.542289

Paper Different receptor models show differences in ligand binding strength and location: a computational drug screening for the tick-borne encephalitis virus.

Finke, Felicitas; Hungerland, Jonathan; Solov'yov, Ilia A et al. · 2025 · Molecular diversity · DOI

Full title: Different receptor models show differences in ligand binding strength and location: a computational drug screening for the tick-borne encephalitis virus.

Authors: Finke, Felicitas; Hungerland, Jonathan; Solov'yov, Ilia A; Schuhmann, Fabian

Year: 2025

Venue: Molecular diversity

DOI: https://doi.org/10.1007/s11030-024-10850-8

Paper Ins and outs of AlphaFold2 transmembrane protein structure predictions

Hegedűs, Tamás; Geisler, Markus; Lukács, Gergely L. et al. · 2022 · Cellular and Molecular Life Sciences · DOI

Full title: Ins and outs of AlphaFold2 transmembrane protein structure predictions

Authors: Hegedűs, Tamás; Geisler, Markus; Lukács, Gergely L.; Farkas, Bianka

Year: 2022

Venue: Cellular and Molecular Life Sciences

DOI: https://doi.org/10.1007/s00018-021-04112-1

Paper Modelling peptide–protein complexes: docking, simulations and machine learning

Mondal, Arup; Chang, Liwei; Pérez, Alberto · 2022 · QRB Discovery · DOI

Full title: Modelling peptide–protein complexes: docking, simulations and machine learning

Authors: Mondal, Arup; Chang, Liwei; Pérez, Alberto

Year: 2022

Venue: QRB Discovery

DOI: https://doi.org/10.1017/qrd.2022.14

Paper Review: Modeling peptide-protein complexes: docking, simulations and machine learning — R0/PR2

Mondal, Arup; Chang, Liwei; Pérez, Alberto · 2022 · DOI

Full title: Review: Modeling peptide-protein complexes: docking, simulations and machine learning — R0/PR2

Authors: Mondal, Arup; Chang, Liwei; Pérez, Alberto

Year: 2022

DOI: https://doi.org/10.1017/qrd.2022.14.pr2

Paper Crystal structure of steroid reductase SRD5A reveals conserved steroid reduction mechanism

Han, Yufei; Zhuang, Qian; Sun, Bo et al. · 2021 · Nature Communications · DOI

Full title: Crystal structure of steroid reductase SRD5A reveals conserved steroid reduction mechanism

Authors: Han, Yufei; Zhuang, Qian; Sun, Bo; Lv, Wenping; Wang, Sheng; Xiao, Qingjie; Pang, Bin; Zhou, Youli; Wang, Fuxing; Chi, Pengliang; Wang, Qisheng; Li, Zhen; Zhu, Lizhe; Li, Fuping; Deng, Dong; Chiang, Ying‐Chih; Li, Zhenfei; Ren, Ruobing

Year: 2021

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-020-20675-2

Paper Structural basis for receptor selectivity and inverse agonism in S1P5 receptors

Lyapina, Elizaveta; Marin, Egor; Gusach, Anastasiia et al. · 2022 · Nature Communications · DOI

Full title: Structural basis for receptor selectivity and inverse agonism in S1P5 receptors

Authors: Lyapina, Elizaveta; Marin, Egor; Gusach, Anastasiia; Orekhov, Philipp S.; Герасимов, А. С.; Luginina, Aleksandra; Vakhrameev, Daniil; Ergasheva, Margarita; Kovaleva, Margarita; Khusainov, Georgii; Khorn, Polina; Shevtsov, M.B.; Kovalev, Kirill; Bukhdruker, Sergey; Okhrimenko, I.S.; Popov, Petr; Hu, Hao; Weierstall, Uwe; Liu, Wei; Cho, Yunje; Gushchin, Ivan; Rogachev, Andrey; Bourenkov, Gleb; Park, Sehan; Park, Gisu; Hyun, Hyo Jung; Park, Jaehyun; Gordeliy, Valentin; Borshchevskiy, Valentin; Mishin, Alexey; Cherezov, Vadim

Year: 2022

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-022-32447-1

Paper Predicting locations of cryptic pockets from single protein structures using the PocketMiner graph neural network

Meller, Artur; Ward, Michael D.; Borowsky, Jonathan et al. · 2023 · Nature Communications · DOI

Full title: Predicting locations of cryptic pockets from single protein structures using the PocketMiner graph neural network

Authors: Meller, Artur; Ward, Michael D.; Borowsky, Jonathan; Kshirsagar, Meghana; Lotthammer, Jeffrey M.; Oviedo, Felipe; Ferres, Juan Lavista; Bowman, Gregory R.

Year: 2023

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-023-36699-3

Paper Biosensor and machine learning-aided engineering of an amaryllidaceae enzyme

d’Oelsnitz, Simon; Diaz, Daniel J.; Kim, Wantae et al. · 2024 · Nature Communications · DOI

Full title: Biosensor and machine learning-aided engineering of an amaryllidaceae enzyme

Authors: d’Oelsnitz, Simon; Diaz, Daniel J.; Kim, Wantae; Acosta, Daniel J.; Dangerfield, Tyler L.; Schechter, Mason W.; Minus, Matthew B.; Howard, James R.; Do, Hannah; Loy, James M.; Alper, Hal S.; Zhang, Yan; Ellington, Andrew D.

Year: 2024

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-024-46356-y

Paper A multicentric consortium study demonstrates that dimethylarginine dimethylaminohydrolase 2 is not a dimethylarginine dimethylaminohydrolase

Ragavan, Vinitha N.; Nair, Pramod C.; Jarzebska, Natalia et al. · 2023 · Nature Communications · DOI

Full title: A multicentric consortium study demonstrates that dimethylarginine dimethylaminohydrolase 2 is not a dimethylarginine dimethylaminohydrolase

Authors: Ragavan, Vinitha N.; Nair, Pramod C.; Jarzebska, Natalia; Angom, Ramcharan Singh; Ruta, Luana; Bianconi, Elisa; Grottelli, Silvia; Tararova, Natalia D.; Ryazanskiy, Daniel; Lentz, Steven R.; Tommasi, Sara; Martens‐Lobenhoffer, Jens; Suzuki-Yamamoto, Toshiko; Kimoto, Masumi; Rubets, Elena; Chau, Sarah; Chen, Yingjie; Hu, Xinli; Bernhardt, Nadine; Spieth, Peter; Weiss, Norbert; Bornstein, Stefan R.; Mukhopadhyay, Debabrata; Bode‐Böger, Stefanie M.; Maas, Renke; Wang, Ying; Macchiarulo, Antonio; Mangoni, Arduino A.; Cellini, Barbara; Rodionov, Roman N.

Year: 2023

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-023-38467-9

Paper Theoretical studies on RNA recognition by Musashi 1 RNA-binding protein

Darai, Nitchakan; Mahalapbutr, Panupong; Wolschann, Peter et al. · 2022 · Scientific Reports · DOI

Full title: Theoretical studies on RNA recognition by Musashi 1 RNA-binding protein

Authors: Darai, Nitchakan; Mahalapbutr, Panupong; Wolschann, Peter; Lee, Vannajan Sanghiran; Wolfinger, Michael T.; Rungrotmongkol, Thanyada

Year: 2022

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-022-16252-w

Paper The determination of the effect(s) of solute carrier family 22-member 2 (SLC22A2) haplotype variants on drug binding via molecular dynamic simulation systems

Abrahams-October, Zainonesa; Johnson, Rabia; Benjeddou, Mongi et al. · 2022 · Scientific Reports · DOI

Full title: The determination of the effect(s) of solute carrier family 22-member 2 (SLC22A2) haplotype variants on drug binding via molecular dynamic simulation systems

Authors: Abrahams-October, Zainonesa; Johnson, Rabia; Benjeddou, Mongi; Cloete, Ruben

Year: 2022

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-022-21291-4

Paper Theoretical studies of arbutin, glutathione, and sea cucumber extracts as inhibitors of tyrosinase.

Zheng, Zheng; Zhang, Shizhuo; Jiang, Tao et al. · 2025 · Scientific reports · DOI

Full title: Theoretical studies of arbutin, glutathione, and sea cucumber extracts as inhibitors of tyrosinase.

Authors: Zheng, Zheng; Zhang, Shizhuo; Jiang, Tao; Liu, Wenlang; Xu, Zifan; Shen, Xinyi; Sun, Tiantian

Year: 2025

Venue: Scientific reports

DOI: https://doi.org/10.1038/s41598-025-06316-y

Paper Before and after AlphaFold2: An overview of protein structure prediction

Bertoline, Letícia M. F.; Lima, Angélica N.; Krieger, José Eduardo et al. · 2023 · Frontiers in Bioinformatics · DOI

Full title: Before and after AlphaFold2: An overview of protein structure prediction

Authors: Bertoline, Letícia M. F.; Lima, Angélica N.; Krieger, José Eduardo; Teixeira, Samantha K.

Year: 2023

Venue: Frontiers in Bioinformatics

DOI: https://doi.org/10.3389/fbinf.2023.1120370

Paper Comprehensive mutations analyses of FTO (fat mass and obesity-associated gene) and their effects on FTO’s substrate binding implicated in obesity

Kumar, Rakesh; Ningombam, Somorjit Singh; Kumar, Rahul et al. · 2022 · Frontiers in Nutrition · DOI

Full title: Comprehensive mutations analyses of FTO (fat mass and obesity-associated gene) and their effects on FTO’s substrate binding implicated in obesity

Authors: Kumar, Rakesh; Ningombam, Somorjit Singh; Kumar, Rahul; Goel, Harsh; Gogia, Ajay; Khurana, Sachin; Deo, S. V. S.; Mathur, Sandeep; Tanwar, Pranay

Year: 2022

Venue: Frontiers in Nutrition

DOI: https://doi.org/10.3389/fnut.2022.852944

Paper A cheminformatics and network pharmacology approach to elucidate the mechanism of action of Mycobacterium tuberculosis γ-carbonic anhydrase inhibitors

A. Manaithiya; R. Bhowmik; Kunal Bhattacharya et al. · 2024 · Frontiers in Pharmacology · DOI

Full title: A cheminformatics and network pharmacology approach to elucidate the mechanism of action of Mycobacterium tuberculosis γ-carbonic anhydrase inhibitors

Authors: A. Manaithiya; R. Bhowmik; Kunal Bhattacharya; Rajarshi Ray; S. S. Shyamal; F. Carta; C. Supuran; Seppo Parkkila; A. Aspatwar

Year: 2024

Venue: Frontiers in Pharmacology

DOI: https://doi.org/10.3389/fphar.2024.1457012

Paper Artificial Intelligence: A New Tool for Structure-Based G Protein-Coupled Receptor Drug Discovery.

Chung, Jason; Hahn, Hyunggu; Flores-Espinoza, Emmanuel et al. · 2025 · Biomolecules · DOI

Full title: Artificial Intelligence: A New Tool for Structure-Based G Protein-Coupled Receptor Drug Discovery.

Authors: Chung, Jason; Hahn, Hyunggu; Flores-Espinoza, Emmanuel; Thomsen, Alex R B

Year: 2025

Venue: Biomolecules

DOI: https://doi.org/10.3390/biom15030423

Paper Structural Characterization and Molecular Dynamics Study of the REPI Fusion Protein from Papaver somniferum L.

Diaz-Bárcena, Alba; Pacios, Luis F.; Giraldo, Patricia · 2023 · Biomolecules · DOI

Full title: Structural Characterization and Molecular Dynamics Study of the REPI Fusion Protein from Papaver somniferum L.

Authors: Diaz-Bárcena, Alba; Pacios, Luis F.; Giraldo, Patricia

Year: 2023

Venue: Biomolecules

DOI: https://doi.org/10.3390/biom14010002

Paper Insight into the Mode of Action of 8-Hydroxyquinoline-Based Blockers on the Histamine Receptor 2

Patel, Amisha; Marquez-Gomez, Paola L.; Torp, Lily R. et al. · 2023 · Biosensors · DOI

Full title: Insight into the Mode of Action of 8-Hydroxyquinoline-Based Blockers on the Histamine Receptor 2

Authors: Patel, Amisha; Marquez-Gomez, Paola L.; Torp, Lily R.; Gao, Lily; Peralta‐Yahya, Pamela

Year: 2023

Venue: Biosensors

DOI: https://doi.org/10.3390/bios13060571

Paper Advances in Computational Intelligence-Based Methods of Structure and Function Prediction of Proteins

Zhang, Jian; Qian, Jingjing · 2024 · Biomolecules · DOI

Full title: Advances in Computational Intelligence-Based Methods of Structure and Function Prediction of Proteins

Authors: Zhang, Jian; Qian, Jingjing

Year: 2024

Venue: Biomolecules

DOI: https://doi.org/10.3390/biom14091083

Paper Exploring Quercetin Hydrate’s Potential as an Antiviral Treatment for Oropouche Virus

Menezes, Gabriela de Lima; Saivish, Marielena Vogel; Sacchetto, Lívia et al. · 2023 · Biophysica · DOI

Full title: Exploring Quercetin Hydrate’s Potential as an Antiviral Treatment for Oropouche Virus

Authors: Menezes, Gabriela de Lima; Saivish, Marielena Vogel; Sacchetto, Lívia; Silva, Gislaine Celestino Dutra da; Teixeira, Igor da Silva; Mistrão, Natalia Franco Bueno; Nogueira, Maurício Lacerda; Oliveira, Jonas Ivan Nobre; Bezerra, Katyanna Sales; Silva, Roosevelt Alves da; Fulco, Umberto L.

Year: 2023

Venue: Biophysica

DOI: https://doi.org/10.3390/biophysica3030032

Paper Limitations of Protein Structure Prediction Algorithms in Therapeutic Protein Development

Niazi, Sarfaraz K.; Mariam, Zamara; Paracha, Rehan Zafar · 2024 · BioMedInformatics · DOI

Full title: Limitations of Protein Structure Prediction Algorithms in Therapeutic Protein Development

Authors: Niazi, Sarfaraz K.; Mariam, Zamara; Paracha, Rehan Zafar

Year: 2024

Venue: BioMedInformatics

DOI: https://doi.org/10.3390/biomedinformatics4010007

Paper Theoretical Studies of Cyanophycin Dipeptides as Inhibitors of Tyrosinases

Krzemińska, Agnieszka; Kwiatos, Natalia; Soares, Franciela Arenhart et al. · 2022 · International Journal of Molecular Sciences · DOI

Full title: Theoretical Studies of Cyanophycin Dipeptides as Inhibitors of Tyrosinases

Authors: Krzemińska, Agnieszka; Kwiatos, Natalia; Soares, Franciela Arenhart; Steinbüchel, Alexander

Year: 2022

Venue: International Journal of Molecular Sciences

DOI: https://doi.org/10.3390/ijms23063335

Paper The Giardial Arginine Deiminase Participates in Giardia-Host Immunomodulation in a Structure-Dependent Fashion via Toll-like Receptors

Fernández‐Lainez, Cynthia; Ji, De; Enríquez‐Flores, Sergio et al. · 2022 · International Journal of Molecular Sciences · DOI

Full title: The Giardial Arginine Deiminase Participates in Giardia-Host Immunomodulation in a Structure-Dependent Fashion via Toll-like Receptors

Authors: Fernández‐Lainez, Cynthia; Ji, De; Enríquez‐Flores, Sergio; García‐Torres, Itzhel; Flores-López, Luis Antonio; Gutiérrez‐Castrellón, Pedro; Vos, Paul de; López‐Velázquez, Gabriel

Year: 2022

Venue: International Journal of Molecular Sciences

DOI: https://doi.org/10.3390/ijms231911552

Paper Computational Study of Molecular Mechanism for the Involvement of Human Serum Albumin in the Renin-Angiotensin-Aldosterone System.

Belinskaia, Daria A; Shestakova, Natalia N; Samodurova, Kamila V et al. · 2024 · International journal of molecular sciences · DOI

Full title: Computational Study of Molecular Mechanism for the Involvement of Human Serum Albumin in the Renin-Angiotensin-Aldosterone System.

Authors: Belinskaia, Daria A; Shestakova, Natalia N; Samodurova, Kamila V; Goncharov, Nikolay V

Year: 2024

Venue: International journal of molecular sciences

DOI: https://doi.org/10.3390/ijms251910260

Paper Modeling and Analysis of HIV-1 Pol Polyprotein as a Case Study for Predicting Large Polyprotein Structures

Hao, Ming; Imamichi, Tomozumi; Chang, Weizhong · 2024 · International Journal of Molecular Sciences · DOI

Full title: Modeling and Analysis of HIV-1 Pol Polyprotein as a Case Study for Predicting Large Polyprotein Structures

Authors: Hao, Ming; Imamichi, Tomozumi; Chang, Weizhong

Year: 2024

Venue: International Journal of Molecular Sciences

DOI: https://doi.org/10.3390/ijms25031809

Paper iBio-GATS—A Semi-Automated Workflow for Structural Modelling of Insect Odorant Receptors

Thanu, Vaanathi Chidambara; Jabeen, Amara; Ranganathan, Shoba · 2024 · International Journal of Molecular Sciences · DOI

Full title: iBio-GATS—A Semi-Automated Workflow for Structural Modelling of Insect Odorant Receptors

Authors: Thanu, Vaanathi Chidambara; Jabeen, Amara; Ranganathan, Shoba

Year: 2024

Venue: International Journal of Molecular Sciences

DOI: https://doi.org/10.3390/ijms25053055

Paper Evaluation of AI-Predicted GH11 Xylanase Models Against a Previously Unreported Experimental Structure: Implications for Conformational Accuracy and Ligand Binding.

Nam, Ki Hyun · 2026 · International journal of molecular sciences · DOI

Full title: Evaluation of AI-Predicted GH11 Xylanase Models Against a Previously Unreported Experimental Structure: Implications for Conformational Accuracy and Ligand Binding.

Authors: Nam, Ki Hyun

Year: 2026

Venue: International journal of molecular sciences

DOI: https://doi.org/10.3390/ijms27031370

Paper Potential Compounds in Indonesian Herbal Plants using Computational Screening for Inhibitory Activity Against Chikungunya Virus Envelope Protein E2

Inda Setyawati; Fatma Ayyalla; Fadhilla Ilyas et al. · 2024 · JURNAL AGRONOMI TANAMAN TROPIKA (JUATIKA) · DOI

Full title: Potential Compounds in Indonesian Herbal Plants using Computational Screening for Inhibitory Activity Against Chikungunya Virus Envelope Protein E2

Authors: Inda Setyawati; Fatma Ayyalla; Fadhilla Ilyas; Mikael Kristiadi; Aprijal Ghiyas; Setiawan

Year: 2024

Venue: JURNAL AGRONOMI TANAMAN TROPIKA (JUATIKA)

DOI: https://doi.org/10.36378/juatika.v6i2.3616

Paper FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction

Alex Morehead; Jianlin Cheng · 2024 · arXiv.org · DOI

Full title: FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction

Authors: Alex Morehead; Jianlin Cheng

Year: 2024

Venue: arXiv.org

DOI: https://doi.org/10.48550/arxiv.2412.10966

Paper Structural and Functional Studies of Proteins Involved in the Regulation of Fatty Acid Metabolism

Zelencova-Gopejenko, Diāna; Zelencova-Gopejenko, Diāna · 2023 · DOI

Full title: Structural and Functional Studies of Proteins Involved in the Regulation of Fatty Acid Metabolism

Authors: Zelencova-Gopejenko, Diāna; Zelencova-Gopejenko, Diāna

Year: 2023

DOI: https://doi.org/10.7250/9789934229121

Paper Harnessing AlphaFold to reveal hERG channel conformational state secrets

Ngo, Khoa; Yang, Pei‐Chi; Yarov‐Yarovoy, Vladimir et al. · 2024 · DOI

Full title: Harnessing AlphaFold to reveal hERG channel conformational state secrets

Authors: Ngo, Khoa; Yang, Pei‐Chi; Yarov‐Yarovoy, Vladimir; Clancy, Colleen E.; Vorobyov, Igor

Year: 2024

DOI: https://doi.org/10.1101/2024.01.27.577468

Paper How Banf1 Functions to Inhibit the Activity of PARP1

Bai, Bond; Bai, Bond · 2024 · DOI

Full title: How Banf1 Functions to Inhibit the Activity of PARP1

Authors: Bai, Bond; Bai, Bond

Year: 2024

DOI: https://doi.org/10.5204/thesis.eprints.254811

Paper MOLECULAR INSIGHTS INTO BINDING BEHAVIOUR OF LAMOTRIGINE WITH INITIATION FACTOR 2 PROTEIN: AN INTEGRATED COMPUTATIONAL STUDIES

Arora, Smriti; Patra, Jeevan · 2022 · DOI

Full title: MOLECULAR INSIGHTS INTO BINDING BEHAVIOUR OF LAMOTRIGINE WITH INITIATION FACTOR 2 PROTEIN: AN INTEGRATED COMPUTATIONAL STUDIES

Authors: Arora, Smriti; Patra, Jeevan

Year: 2022

DOI: https://doi.org/10.1101/2022.08.26.505506

Thesis An overview of data-driven HADDOCK strategies in CAPRI rounds 38-45

Koukos, Panagiotis I.; Roel-Touris, Jorge; Ambrosetti, Francesco et al. · 2020 · Utrecht University · DOI

Full title: An overview of data-driven HADDOCK strategies in CAPRI rounds 38-45

Authors: Koukos, Panagiotis I.; Roel-Touris, Jorge; Ambrosetti, Francesco; Geng, Cunliang; Schaarschmidt, Jorg; Trellet, Mikael E.; Melquiond, Adrien S. J.; Xue, Li C.; Honorato, Rodrigo V.; Moreira, Irina; Kurkcuoglu, Zeynep; Vangone, Anna; Bonvin, Alexandre M. J. J.

Year: 2020

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/390638

Thesis Development of Computer Aided Drug Design Algorithms and Application to be APOBEC3 Family of Proteins

Wagner, Jeffrey Robert Rothfeld · 2018 · University of California, San Diego (UCSD) · DOI

Full title: Development of Computer Aided Drug Design Algorithms and Application to be APOBEC3 Family of Proteins

Authors: Wagner, Jeffrey Robert Rothfeld

Year: 2018

Venue: University of California, San Diego (UCSD)

DOI: https://escholarship.org/uc/item/9c66d756

Thesis New approaches to accelerate structure-based small molecule discovery

Flynn, Alex James · 2023 · White Rose eTheses (Leeds, Sheffield, York) · DOI

Full title: New approaches to accelerate structure-based small molecule discovery

Authors: Flynn, Alex James

Year: 2023

Venue: White Rose eTheses (Leeds, Sheffield, York)

DOI: https://etheses.whiterose.ac.uk/id/eprint/34242/1/AF%20corrected%20thesis%20for%20upload.pdf

Thesis Deep learning approaches for conformational flexibility and switching properties in protein design

Rudden, Lucas S. P.; Hijazi, Mahdi; Barth, Patrick · 2022 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Deep learning approaches for conformational flexibility and switching properties in protein design

Authors: Rudden, Lucas S. P.; Hijazi, Mahdi; Barth, Patrick

Year: 2022

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/190456

Thesis Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures

Kwon, S; Safer, J; Nguyen, DT et al. · 2025 · University of Melbourne · DOI

Full title: Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures

Authors: Kwon, S; Safer, J; Nguyen, DT; Hoksza, D; May, P; Arbesfeld, JA; Rubin, AF; Campbell, AJ; Burgin, A; Iqbal, S

Year: 2025

Venue: University of Melbourne

DOI: https://hdl.handle.net/11343/358701

Thesis Machine Learning for Kinase Drug Discovery

Kimber, Talia Beatrice · 2023 · Freie Universität Berlin (Refubium) · DOI

Full title: Machine Learning for Kinase Drug Discovery

Authors: Kimber, Talia Beatrice

Year: 2023

Venue: Freie Universität Berlin (Refubium)

DOI: https://refubium.fu-berlin.de/handle/fub188/38039

Thesis Defining the limits of homology modeling in information-driven protein docking

Garcia Lopes Maia Rodrigues, João; Melquiond, A S J; Karaca, E et al. · 2013 · Utrecht University · DOI

Full title: Defining the limits of homology modeling in information-driven protein docking

Authors: Garcia Lopes Maia Rodrigues, João; Melquiond, A S J; Karaca, E; Trellet, M; van Dijk, M; van Zundert, G C P; Schmitz, C; de Vries, S J; Bordogna, A; Bonati, L; Kastritis, P L; Bonvin, Alexandre M J J; Garcia Lopes Maia Rodrigues, João

Year: 2013

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/290387

Thesis Next challenges in protein–protein docking: from proteome to interactome and beyond

Melquiond, A.S.J.; Karaca, E.; Kastritis, P. et al. · 2012 · Utrecht University · DOI

Full title: Next challenges in protein–protein docking: from proteome to interactome and beyond

Authors: Melquiond, A.S.J.; Karaca, E.; Kastritis, P.; Bonvin, A.M.J.J.

Year: 2012

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/255698

Thesis Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2

Vreven, Thom; Moal, Iain H.; Vangone, Anna et al. · 2015 · Utrecht University · DOI

Full title: Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2

Authors: Vreven, Thom; Moal, Iain H.; Vangone, Anna; Pierce, Brian G.; Kastritis, Panagiotis L.; Torchala, Mieczyslaw; Chaleil, Raphael; Jiménez-García, Brian; Bates, Paul A.; Fernandez-Recio, Juan; Bonvin, Alexandre M J J; Weng, Zhiping

Year: 2015

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/354214

Thesis A benchmark testing ground for integrating homology modeling and protein docking

Bohnuud, Tanggis; Luo, Lingqi; Wodak, Shoshana J et al. · 2017 · Utrecht University · DOI

Full title: A benchmark testing ground for integrating homology modeling and protein docking

Authors: Bohnuud, Tanggis; Luo, Lingqi; Wodak, Shoshana J; Bonvin, Alexandre M J J; Weng, Zhiping; Vajda, Sandor; Schueler-Furman, Ora; Kozakov, Dima

Year: 2017

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/344418

Thesis Membrane proteins structures: A review on computational modeling tools

Almeida, Jose G; Preto, Antonio J.; Koukos, Panos et al. · 2017 · Utrecht University · DOI

Full title: Membrane proteins structures: A review on computational modeling tools

Authors: Almeida, Jose G; Preto, Antonio J.; Koukos, Panos; Bonvin, Alexandre M.J.J.; de Sousa Moreira, Irina

Year: 2017

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/363472

Thesis Folding Then Binding vs Folding Through Binding in Macrocyclic Peptide Inhibitors of Human Pancreatic α-Amylase

Goldbach, Leander; Vermeulen, Bram J A; Caner, Sami et al. · 2019 · Utrecht University · DOI

Full title: Folding Then Binding vs Folding Through Binding in Macrocyclic Peptide Inhibitors of Human Pancreatic α-Amylase

Authors: Goldbach, Leander; Vermeulen, Bram J A; Caner, Sami; Liu, Minglong; Tysoe, Christina; van Gijzel, Lieke; Yoshisada, Ryoji; Trellet, Mikael; van Ingen, Hugo; Brayer, Gary D; Bonvin, Alexandre M J J; Jongkees, Seino A K

Year: 2019

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/384217

Thesis Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape

Basciu, Andrea; Malloci, Giuliano; Pietrucci, Fabio et al. · 2019 · Utrecht University · DOI

Full title: Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape

Authors: Basciu, Andrea; Malloci, Giuliano; Pietrucci, Fabio; Bonvin, Alexandre M.J.J.; Vargiu, Attilio V.

Year: 2019

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/387042

Thesis Pre- and post-docking sampling of conformational changes using ClustENM and HADDOCK for protein-protein and protein-DNA systems

Kurkcuoglu, Zeynep; Bonvin, Alexandre M.J.J. · 2020 · Utrecht University · DOI

Full title: Pre- and post-docking sampling of conformational changes using ClustENM and HADDOCK for protein-protein and protein-DNA systems

Authors: Kurkcuoglu, Zeynep; Bonvin, Alexandre M.J.J.

Year: 2020

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/391763

Thesis Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4

Basciu, Andrea; Koukos, Panagiotis I; Malloci, Giuliano et al. · 2020 · Utrecht University · DOI

Full title: Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4

Authors: Basciu, Andrea; Koukos, Panagiotis I; Malloci, Giuliano; Bonvin, Alexandre M J J; Vargiu, Attilio V

Year: 2020

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/391767

Thesis Impact of AlphaFold on Structure Prediction of Protein Complexes: The CASP15-CAPRI Experiment

Lensink, Marc; Brysbaert, Guillaume; Raouraoua, Nessim et al. · 2023 · Utrecht University · DOI

Full title: Impact of AlphaFold on Structure Prediction of Protein Complexes: The CASP15-CAPRI Experiment

Authors: Lensink, Marc; Brysbaert, Guillaume; Raouraoua, Nessim; Bates, Paul; Giulini, Marco; Honorato, Rodrigo Vargas; Noort, Charlotte van; Teixeira, João; Bonvin, Alexandre M.J.J.; Kong, Ren; Shi, Hang; Lu, Xufeng; Chang, Shan; Liu, Jian; Guo, Zhiye; Chen, Xiao; Morehead, Alex; Roy, Raj; Wu, Tianqi; Giri, Nabin; Quadir, Farhan; Chen, Chen; Cheng, Jianlin; Carpio, Carlos Del; Ichiishi, Eichiro; Luis, Rodriguez-Lumbreras A; Fernández-Recio, Juan; Harmalkar, Ameya; Chu, Lee-Shin; Canner, Sam; Smanta, Rituparna; Gray, Jeffrey; Li, Hao; Lin, Peicong; He, Jiahua; Tao, Huanyu; Huang, Shengyou; Roel, Jorge; Jimenez-Garcia, Brian; Christoffer, Charles; Anika, Jain J; Kagaya, Yuki; Kannan, Harini; Nakamura, Tsukasa; Terashi, Genki; Verburgt, Jacob; Zhang, Yuanyuan; Zhang, Zicong; Fujuta, Hayato; Sekijima, Masakazu; Kihara, Daisuke; Khan, Omeir; Kotelnikov, Sergei; Ghani, Usman; Padhorny, Dzmitry; Beglov, Dmitri; Vajda, Sandor; Kozakov, Dima; Surendra, Negi S; Ricciardelli, Tiziana; Barradas-Bautista, Didier; Cao, Zhen; Chawla, Mohit; Cavallo, Luigi; Oliva, Romina; Yin, Rujie; Cheung, Melyssa; Guest, Johnathan; Lee, Jessica; Pierce, Brian; Shor, Ben; Cohen, Tomer; Halfon, Matan; Schneidman-Duhovny, Dina; Zhu, Shaowen; Yin, Rujie; Sun, Yuanfei; Shen, Yang; Maszota-Zieleniak, Martyna; Krzysztof, Bojarski K; Lubecka, Emilia; Marcisz, Mateusz; Danielsson, Annemarie; Dziadek, Lukasz; Gaardlos, Margrethe; Giełdoń, Artur; Liwo, Jozef; Samsonov, Sergey; Slusarz, Rafal; Zieba, Karolina; Sieradzan, Adam; Czaplewski, Cezary; Kobayashi, Shinpei; Miyakawa, Yuta; Kiyota, Yasuomi; Takeda-Shitaka, Mayuko; Olechnovič, Kliment; Valančauskas, Lukas; Dapkūnas, Justas; Venclovas, Ceslovas; Wallner, Björn; Yang, Lin; Hou, Chengyu; He, Xiaodong; Guo, Shuai; Jiang, Shenda; Ma, Xiaoliang; Duan, Rui; Qiu, Liming; Xu, Xianjin; Zou, Xiaoqin; Velankar, Sameer; Shoshana, Wodak J

Year: 2023

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/438081

Thesis DeepRank-GNN: A Graph Neural Network Framework to Learn Patterns in Protein-Protein Interfaces

Réau, Manon; Renaud, Nicolas; Xue, Li C et al. · 2023 · Utrecht University · DOI

Full title: DeepRank-GNN: A Graph Neural Network Framework to Learn Patterns in Protein-Protein Interfaces

Authors: Réau, Manon; Renaud, Nicolas; Xue, Li C; Bonvin, Alexandre M J J

Year: 2023

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/425720

Thesis Improving the quality of co-evolution intermolecular contact prediction with DisVis

van Keulen, Siri C.; Bonvin, Alexandre M.J.J. · 2023 · Utrecht University · DOI

Full title: Improving the quality of co-evolution intermolecular contact prediction with DisVis

Authors: van Keulen, Siri C.; Bonvin, Alexandre M.J.J.

Year: 2023

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/434156

Thesis Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study

Schweke, Hugo; Xu, Qifang; Tauriello, Gerardo et al. · 2023 · Utrecht University · DOI

Full title: Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study

Authors: Schweke, Hugo; Xu, Qifang; Tauriello, Gerardo; Pantolini, Lorenzo; Schwede, Torsten; Cazals, Frédéric; Lhéritier, Alix; Fernandez-Recio, Juan; Rodríguez-Lumbreras, Luis Angel; Schueler-Furman, Ora; Varga, Julia K.; Jiménez-García, Brian; Réau, Manon F.; Bonvin, Alexandre M.J.J.; Savojardo, Castrense; Martelli, Pier Luigi; Casadio, Rita; Tubiana, Jérôme; Wolfson, Haim J.; Oliva, Romina; Barradas-Bautista, Didier; Ricciardelli, Tiziana; Cavallo, Luigi; Venclovas, Česlovas; Olechnovič, Kliment; Guerois, Raphael; Andreani, Jessica; Martin, Juliette; Wang, Xiao; Terashi, Genki; Sarkar, Daipayan; Christoffer, Charles; Aderinwale, Tunde; Verburgt, Jacob; Kihara, Daisuke; Marchand, Anthony; Correia, Bruno E.; Duan, Rui; Qiu, Liming; Xu, Xianjin; Zhang, Shuang; Zou, Xiaoqin; Dey, Sucharita; Dunbrack, Roland L.; Levy, Emmanuel D.; Wodak, Shoshana J.

Year: 2023

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/434203

Thesis MetaScore: A Novel Machine-Learning-Based Approach to Improve Traditional Scoring Functions for Scoring Protein-Protein Docking Conformations

Jung, Yong; Geng, Cunliang; Bonvin, Alexandre M. J. J. et al. · 2023 · Utrecht University · DOI

Full title: MetaScore: A Novel Machine-Learning-Based Approach to Improve Traditional Scoring Functions for Scoring Protein-Protein Docking Conformations

Authors: Jung, Yong; Geng, Cunliang; Bonvin, Alexandre M. J. J.; Xue, Li C.; Honavar, Vasant G.

Year: 2023

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/436107

Thesis Casting Protein Structure Predictors as Energy-Based Models for Binder Design and Scoring

Nori, Divya · 2025 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Casting Protein Structure Predictors as Energy-Based Models for Binder Design and Scoring

Authors: Nori, Divya

Year: 2025

Venue: Massachusetts Institute of Technology (MIT)

DOI: https://hdl.handle.net/1721.1/162975

Thesis Comparing Native Crystal Structures and AlphaFold2 Predicted Water-Soluble G Protein-Coupled Receptor QTY Variants

Skuhersky, Michael A.; Tao, Fei; Qing, Rui et al. · 2021 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Comparing Native Crystal Structures and AlphaFold2 Predicted Water-Soluble G Protein-Coupled Receptor QTY Variants

Authors: Skuhersky, Michael A.; Tao, Fei; Qing, Rui; Smorodina, Eva; Jin, David; Zhang, Shuguang

Year: 2021

Venue: Massachusetts Institute of Technology (MIT)

DOI: https://hdl.handle.net/1721.1/138236

Thesis Inference Time Search for Protein Structure Prediction

Qi, Richard · 2025 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Inference Time Search for Protein Structure Prediction

Authors: Qi, Richard

Year: 2025

Venue: Massachusetts Institute of Technology (MIT)

DOI: https://hdl.handle.net/1721.1/162989

Thesis Structure Prediction and Virtual Screening: Application to G Protein-coupled Receptors

Marko, Adam Christian · 2009 · University of California, San Francisco (UCSF) · DOI

Full title: Structure Prediction and Virtual Screening: Application to G Protein-coupled Receptors

Authors: Marko, Adam Christian

Year: 2009

Venue: University of California, San Francisco (UCSF)

DOI: https://escholarship.org/uc/item/1cz1433r

Thesis Determination of X-ray Crystal Structure of Human E3 Ligase in Complex with Small Molecule Ligands

Huang, Shih-Ting · 2022 · University of California, San Diego (UCSD) · DOI

Full title: Determination of X-ray Crystal Structure of Human E3 Ligase in Complex with Small Molecule Ligands

Authors: Huang, Shih-Ting

Year: 2022

Venue: University of California, San Diego (UCSD)

DOI: https://escholarship.org/uc/item/1ss6x4k0

Thesis The Nobel Prize in Chemistry: past, present, and future of AI in biology

Abriata, Luciano A. · 2025 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: The Nobel Prize in Chemistry: past, present, and future of AI in biology

Authors: Abriata, Luciano A.

Year: 2025

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/245542

Thesis One-shot Design of Functional Protein Binders with Bindcraft

Pacesa, Martin; Nickel, Lennart; Schellhaas, Christian et al. · 2025 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: One-shot Design of Functional Protein Binders with Bindcraft

Authors: Pacesa, Martin; Nickel, Lennart; Schellhaas, Christian; Schmidt, Joseph; Pyatova, Ekaterina; Kissling, Lucas; Barendse, Patrick; Choudhury, Jagrity; Kapoor, Srajan; Alcaraz-Serna, Ana; Cho, Yehlin; Ghamary, Kourosh H.; Vinue, Laura; Yachnin, Brahm J.; Wollacott, Andrew M.; Buckley, Stephen; Westphal, Adrie H.; Lindhoud, Simon; Georgeon, Sandrine; Goverde, Casper A.; Hatzopoulos, Georgios N.; Gonczy, Pierre; Muller, Yannick D.; Schwank, Gerald; Swarts, Daan C.; Vecchio, Alex J.; Schneider, Bernard L.; Ovchinnikov, Sergey; Correia, Bruno E.

Year: 2025

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/253809

Thesis Computational modeling of the olfactory receptor Olfr73 suggests a molecular basis for low potency of olfactory receptor-activating compounds

Yuan, Shuguang; Dahoun, Thamani; Brugarolas, Marc et al. · 2019 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Computational modeling of the olfactory receptor Olfr73 suggests a molecular basis for low potency of olfactory receptor-activating compounds

Authors: Yuan, Shuguang; Dahoun, Thamani; Brugarolas, Marc; Pick, Horst; Filipek, Slawomir; Vogel, Horst

Year: 2019

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/157572

Thesis Expanding the boundaries of ligand-target modeling by exascale calculations

Bolnykh, Viacheslav; Rossetti, Giulia; Rothlisberger, Ursula et al. · 2021 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Expanding the boundaries of ligand-target modeling by exascale calculations

Authors: Bolnykh, Viacheslav; Rossetti, Giulia; Rothlisberger, Ursula; Carloni, Paolo

Year: 2021

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/178275

Thesis COMPUTATIONAL TECHNIQUES TO EVALUATE AT ATOMIC LEVEL THE MECHANISM OF MOLECULAR BINDING

C. Paissoni · 2017 · Università degli Studi di Milano (AIR) · DOI

Full title: COMPUTATIONAL TECHNIQUES TO EVALUATE AT ATOMIC LEVEL THE MECHANISM OF MOLECULAR BINDING

Authors: C. Paissoni

Year: 2017

Venue: Università degli Studi di Milano (AIR)

DOI: http://hdl.handle.net/2434/480031

Thesis Protein Structure Accuracy Prediction with Deep Learning and its Application to Structure Prediction and Design

Hiranuma, Naozumi · 2022 · University of Washington - ResearchWorks · DOI

Full title: Protein Structure Accuracy Prediction with Deep Learning and its Application to Structure Prediction and Design

Authors: Hiranuma, Naozumi

Year: 2022

Venue: University of Washington - ResearchWorks

DOI: http://hdl.handle.net/1773/48478

Thesis Developing a high throughput in silico screening pipeline for the discovery of novel antifungals

Hambly, Jacob · 2025 · University of Guelph · DOI

Full title: Developing a high throughput in silico screening pipeline for the discovery of novel antifungals

Authors: Hambly, Jacob

Year: 2025

Venue: University of Guelph

DOI: https://hdl.handle.net/10214/29207

Thesis How proteins get in touch: Interface prediction and docking of protein complexes

de Vries, S.J. · 2009 · Utrecht University · DOI

Full title: How proteins get in touch: Interface prediction and docking of protein complexes

Authors: de Vries, S.J.

Year: 2009

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/33805

Thesis Modelling protein-DNA interactions: bend and twist until it fits

van Dijk, M. · 2010 · Utrecht University · DOI

Full title: Modelling protein-DNA interactions: bend and twist until it fits

Authors: van Dijk, M.

Year: 2010

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/40020

Thesis Computational methods for the structure-based design of protein-binding peptides

Swanson, Sebastian Robles · 2023 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Computational methods for the structure-based design of protein-binding peptides

Authors: Swanson, Sebastian Robles

Year: 2023

Venue: Massachusetts Institute of Technology (MIT)

DOI: https://hdl.handle.net/1721.1/153028

Thesis Biomolecular Modeling at Scale

Wohlwend, Jeremy · 2025 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Biomolecular Modeling at Scale

Authors: Wohlwend, Jeremy

Year: 2025

Venue: Massachusetts Institute of Technology (MIT)

DOI: https://hdl.handle.net/1721.1/164122

Thesis Modeling Biomolecular Interactions with Generative Models

Corso, Gabriele · 2025 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Modeling Biomolecular Interactions with Generative Models

Authors: Corso, Gabriele

Year: 2025

Venue: Massachusetts Institute of Technology (MIT)

DOI: https://hdl.handle.net/1721.1/164058

Thesis Integrating conformational and protonation equilibria in biomolecular modeling

Kim, Meekyum Olivia · 2015 · University of California, San Diego (UCSD) · DOI

Full title: Integrating conformational and protonation equilibria in biomolecular modeling

Authors: Kim, Meekyum Olivia

Year: 2015

Venue: University of California, San Diego (UCSD)

DOI: https://escholarship.org/uc/item/0rp5481g

Thesis Physics-based Refinement of Proteins in Model Systems

Sellers, Benjamin D · 2008 · University of California, San Francisco (UCSF) · DOI

Full title: Physics-based Refinement of Proteins in Model Systems

Authors: Sellers, Benjamin D

Year: 2008

Venue: University of California, San Francisco (UCSF)

DOI: https://escholarship.org/uc/item/1tv93190

Thesis Ligand Desolvation in Molecular Docking (How, Why, and With What?)

Mysinger, Michael McLeod · 2012 · University of California, San Francisco (UCSF) · DOI

Full title: Ligand Desolvation in Molecular Docking (How, Why, and With What?)

Authors: Mysinger, Michael McLeod

Year: 2012

Venue: University of California, San Francisco (UCSF)

DOI: https://escholarship.org/uc/item/24t6017j

Thesis Improved prediction of structurally diverse de novo proteins

Orr, Benjamin David · 2025 · University of California, San Francisco (UCSF) · DOI

Full title: Improved prediction of structurally diverse de novo proteins

Authors: Orr, Benjamin David

Year: 2025

Venue: University of California, San Francisco (UCSF)

DOI: https://escholarship.org/uc/item/6r869912

Thesis Computational biochemical approaches to protein structure prediction and drug discovery

Biehn, Sarah Elizabeth · 2022 · OhioLINK Electronic Theses and Dissertations · DOI

Full title: Computational biochemical approaches to protein structure prediction and drug discovery

Authors: Biehn, Sarah Elizabeth

Year: 2022

Venue: OhioLINK Electronic Theses and Dissertations

DOI: http://rave.ohiolink.edu/etdc/view?acc_num=osu1649673976879668

Thesis Advancing Computational Protein Modeling: Sparse Data Integration in Rosetta and AlphaFold2

Drake, Zachary Colton · 2025 · OhioLINK Electronic Theses and Dissertations · DOI

Full title: Advancing Computational Protein Modeling: Sparse Data Integration in Rosetta and AlphaFold2

Authors: Drake, Zachary Colton

Year: 2025

Venue: OhioLINK Electronic Theses and Dissertations

DOI: http://rave.ohiolink.edu/etdc/view?acc_num=osu1752424969978784

Thesis Structural and pharmacological analysis of novel adenosine A2A receptor ligands to guide rational drug design

Zilian, Claudia Tania · 2022 · White Rose eTheses (Leeds, Sheffield, York) · DOI

Full title: Structural and pharmacological analysis of novel adenosine A2A receptor ligands to guide rational drug design

Authors: Zilian, Claudia Tania

Year: 2022

Venue: White Rose eTheses (Leeds, Sheffield, York)

DOI: https://etheses.whiterose.ac.uk/id/eprint/30804/1/Zilian_CT_Biomedical-Sciences_PhD_2022.pdf

Thesis Discrete approaches for leveraging g protein-coupled receptors as therapeutic tools

Marcus Saarinen (18666955) · 2024 · Karolinska Institutet · DOI

Full title: Discrete approaches for leveraging g protein-coupled receptors as therapeutic tools

Authors: Marcus Saarinen (18666955)

Year: 2024

Venue: Karolinska Institutet

DOI: oai:figshare.com:article/27055156

Thesis Insights on Protein Conformational Diversity at the Ligand Binding Site Level

Feidakis, Christos · 2025 · Charles University Prague (Univerzita Karlova) · DOI

Full title: Insights on Protein Conformational Diversity at the Ligand Binding Site Level

Authors: Feidakis, Christos

Year: 2025

Venue: Charles University Prague (Univerzita Karlova)

DOI: http://hdl.handle.net/20.500.11956/196368

Thesis Generative Modeling of Full-Atom Protein Conformations using Latent Diffusion on Graph Embeddings

Sengar, Aditya; Hariri, Ali; Probst, Daniel et al. · 2025 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Generative Modeling of Full-Atom Protein Conformations using Latent Diffusion on Graph Embeddings

Authors: Sengar, Aditya; Hariri, Ali; Probst, Daniel; Barth, Patrick; Vandergheynst, Pierre

Year: 2025

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/251548

Thesis A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer

Krapp, Lucien Fabrice · 2023 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer

Authors: Krapp, Lucien Fabrice

Year: 2023

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/201949

Thesis Protein target highlights in CASP15: Analysis of models by structure providers

Alexander, Leila T.; Durairaj, Janani; Kryshtafovych, Andriy et al. · 2023 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Protein target highlights in CASP15: Analysis of models by structure providers

Authors: Alexander, Leila T.; Durairaj, Janani; Kryshtafovych, Andriy; Abriata, Luciano A.; Bayo, Yusupha; Bhabha, Gira; Breyton, Cecile; Caulton, Simon G.; Chen, James; Degroux, Seraphine; Ekiert, Damian C.; Erlandsen, Benedikte S.; Freddolino, Peter L.; Gilzer, Dominic; Greening, Chris; Grimes, Jonathan M.; Grinter, Rhys; Gurusaran, Manickam; Hartmann, Marcus D.; Hitchman, Charlie J.; Keown, Jeremy R.; Kropp, Ashleigh; Kursula, Petri; Lovering, Andrew L.; Lemaitre, Bruno; Lia, Andrea; Liu, Shiheng; Logotheti, Maria; Lu, Shuze; Markusson, Sigurbjorn; Miller, Mitchell D.; Minasov, George; Niemann, Hartmut H.; Opazo, Felipe; Phillips Jr, George N. N.; Davies, Owen R.; Rommelaere, Samuel; Rosas-Lemus, Monica; Roversi, Pietro; Satchell, Karla; Smith, Nathan; Wilson, Mark A.; Wu, Kuan-Lin; Xia, Xian; Xiao, Han; Zhang, Wenhua; Zhou, Z. Hong; Fidelis, Krzysztof; Topf, Maya; Moult, John; Schwede, Torsten

Year: 2023

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/199869

Thesis Computational modeling, prediction, and design of Protein-Protein interactions

Harmalkar, Ameya Uddhav · 2023 · Johns Hopkins University · DOI

Full title: Computational modeling, prediction, and design of Protein-Protein interactions

Authors: Harmalkar, Ameya Uddhav

Year: 2023

Venue: Johns Hopkins University

DOI: http://jhir.library.jhu.edu/handle/1774.2/68944

Thesis Predicting protein interactions using geometric deep learning on protein surfaces

Sverrisson, Freyr · 2024 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Predicting protein interactions using geometric deep learning on protein surfaces

Authors: Sverrisson, Freyr

Year: 2024

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/206239

Thesis Protein Target Highlights in CASP16 : Insights From the Structure Providers

None · 2025 · University of Melbourne · DOI

Full title: Protein Target Highlights in CASP16 : Insights From the Structure Providers

Authors: None

Year: 2025

Venue: University of Melbourne

DOI: https://hdl.handle.net/11343/362434

Thesis The new insights into protein structures by computational methods

Zou, Ye · 2022 · Kansas State University - K-REx · DOI

Full title: The new insights into protein structures by computational methods

Authors: Zou, Ye

Year: 2022

Venue: Kansas State University - K-REx

DOI: https://hdl.handle.net/2097/42225

Thesis The application of advanced structural bioinformatics methods to parasitic membrane proteins

Murphy, David · 2024 · University of Liverpool · DOI

Full title: The application of advanced structural bioinformatics methods to parasitic membrane proteins

Authors: Murphy, David

Year: 2024

Venue: University of Liverpool

DOI: https://livrepository.liverpool.ac.uk/3182410/1/201365014_Jun2024.pdf

Thesis Interdisciplinary techniques in protein binding prediction and crystal engineering

DeRoo, Jacob Benjamin, author; Reynolds, Melissa, advisor; Snow, Christopher D., advisor et al. · 2024 · Colorado State University · DOI

Full title: Interdisciplinary techniques in protein binding prediction and crystal engineering

Authors: DeRoo, Jacob Benjamin, author; Reynolds, Melissa, advisor; Snow, Christopher D., advisor; Reardon, Ken, committee member; Zabel, Mark, committee member

Year: 2024

Venue: Colorado State University

DOI: https://hdl.handle.net/10217/239831

Thesis Structural Analysis of 20S Proteasome and Development of Structure-Based Virtual Screening Methods

Arciniega Castro, Marcelino · 2014 · Technical University of Munich · DOI

Full title: Structural Analysis of 20S Proteasome and Development of Structure-Based Virtual Screening Methods

Authors: Arciniega Castro, Marcelino

Year: 2014

Venue: Technical University of Munich

DOI: https://mediatum.ub.tum.de/1221441

Thesis Impact of Protein conformational Changes on Molecular Docking - Design of a Docking Approach including Receptor Flexibility

Leis, Simon · 2013 · Technical University of Munich · DOI

Full title: Impact of Protein conformational Changes on Molecular Docking - Design of a Docking Approach including Receptor Flexibility

Authors: Leis, Simon

Year: 2013

Venue: Technical University of Munich

DOI: https://mediatum.ub.tum.de/1115345

Thesis Quality assessment of docked protein interfaces using 3D convolution

Bontha, Mridula, author; Ben-Hur, Asa, advisor; Beveridge, J. Ross, committee member et al. · 2021 · Colorado State University · DOI

Full title: Quality assessment of docked protein interfaces using 3D convolution

Authors: Bontha, Mridula, author; Ben-Hur, Asa, advisor; Beveridge, J. Ross, committee member; King, Emily J., committee member

Year: 2021

Venue: Colorado State University

DOI: https://hdl.handle.net/10217/232476

Thesis Deep Learning Tools for Protein Binder Design

Bennett, Nathaniel · 2023 · University of Washington - ResearchWorks · DOI

Full title: Deep Learning Tools for Protein Binder Design

Authors: Bennett, Nathaniel

Year: 2023

Venue: University of Washington - ResearchWorks

DOI: http://hdl.handle.net/1773/50187

Thesis Enhancing Protein Sequence Design through Augmented Machine Learning of Hydrogen Bonding Networks

Tan, Kevin · 2024 · Harvard University - DASH · DOI

Full title: Enhancing Protein Sequence Design through Augmented Machine Learning of Hydrogen Bonding Networks

Authors: Tan, Kevin

Year: 2024

Venue: Harvard University - DASH

DOI: https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37379285

Thesis CSM-Potential: mapping protein interactions and biological ligands in 3D space using geometric deep learning

Rodrigues, CHM; Ascher, DB · 2022 · University of Melbourne · DOI

Full title: CSM-Potential: mapping protein interactions and biological ligands in 3D space using geometric deep learning

Authors: Rodrigues, CHM; Ascher, DB

Year: 2022

Venue: University of Melbourne

DOI: https://hdl.handle.net/11343/316133

Thesis Optimization of protein-protein docking for predicting Fc-protein interactions

Agostino, M; Mancera, RL; Ramsland, PA et al. · 2021 · University of Melbourne · DOI

Full title: Optimization of protein-protein docking for predicting Fc-protein interactions

Authors: Agostino, M; Mancera, RL; Ramsland, PA; Fernández-Recio, J

Year: 2021

Venue: University of Melbourne

DOI: https://hdl.handle.net/11343/291528

Thesis Structure-Based Discovery of Lipoteichoic Acid Synthase Inhibitors

Wezen, Xavier Chee; Chandran, Aneesh; Eapen, Rohan Sakariah et al. · 2022 · University of Liverpool · DOI

Full title: Structure-Based Discovery of Lipoteichoic Acid Synthase Inhibitors

Authors: Wezen, Xavier Chee; Chandran, Aneesh; Eapen, Rohan Sakariah; Waters, Elaine; Bricio-Moreno, Laura; Tosi, Tommaso; Dolan, Stephen; Millership, Charlotte; Kadioglu, Aras; Grundling, Angelika; Itzhaki, Laura S; Welch, Martin; Rahman, Taufiq

Year: 2022

Venue: University of Liverpool

DOI: https://livrepository.liverpool.ac.uk/3158905/1/Structure-Based%20Discovery%20of%20Lipoteichoic%20Acid%20Synthase%20Inhibitors.pdf

Thesis Using Molecular Dynamics and Enhanced Sampling to Predict Binding Poses Beyond The Rigid-Docking Approximation

Åberg, Emil · 2017 · Lund University Student Papers · DOI

Full title: Using Molecular Dynamics and Enhanced Sampling to Predict Binding Poses Beyond The Rigid-Docking Approximation

Authors: Åberg, Emil

Year: 2017

Venue: Lund University Student Papers

DOI: http://lup.lub.lu.se/student-papers/record/8903956

Thesis Quality assessment of protein structures using graph convolutional networks

Roy, Soumyadip, author; Ben-Hur, Asa, advisor; Blanchard, Nathaniel, committee member et al. · 2024 · Colorado State University · DOI

Full title: Quality assessment of protein structures using graph convolutional networks

Authors: Roy, Soumyadip, author; Ben-Hur, Asa, advisor; Blanchard, Nathaniel, committee member; Zhou, Wen, committee member

Year: 2024

Venue: Colorado State University

DOI: https://hdl.handle.net/10217/238364

Thesis Adapting molecular docking to study sialylated glycans

Hu, Huimin · 2024 · University of Georgia - UGA Open Scholar · DOI

Full title: Adapting molecular docking to study sialylated glycans

Authors: Hu, Huimin

Year: 2024

Venue: University of Georgia - UGA Open Scholar

DOI: https://openscholar.uga.edu/record/8501/files/hu_huimin_201512_ms.pdf

Thesis Accelerating Protein Design with Deep Learning

McPartlon, Matthew Timothy · 2023 · University of Chicago - Knowledge@UChicago · DOI

Full title: Accelerating Protein Design with Deep Learning

Authors: McPartlon, Matthew Timothy

Year: 2023

Venue: University of Chicago - Knowledge@UChicago

DOI: https://knowledge.uchicago.edu/record/7659/files/McPartlon_uchicago_0330D_16988.pdf

Thesis Mechanistic Characterization and Development of Tailored Small Molecule Modulators of the κ-Opioid Receptor

Puls, Kristina · 2024 · Freie Universität Berlin (Refubium) · DOI

Full title: Mechanistic Characterization and Development of Tailored Small Molecule Modulators of the κ-Opioid Receptor

Authors: Puls, Kristina

Year: 2024

Venue: Freie Universität Berlin (Refubium)

DOI: https://refubium.fu-berlin.de/handle/fub188/43919

Thesis Investigations on Key Principles of PTP1B Selectivity

Naß, Alexandra · 2018 · Freie Universität Berlin (Refubium) · DOI

Full title: Investigations on Key Principles of PTP1B Selectivity

Authors: Naß, Alexandra

Year: 2018

Venue: Freie Universität Berlin (Refubium)

DOI: https://refubium.fu-berlin.de/handle/fub188/22198

Thesis Computational approaches exploring the structure and dynamics of ligand-gated ion channel receptors.

Chen, Zheng · 2023 · University of Sydney · DOI

Full title: Computational approaches exploring the structure and dynamics of ligand-gated ion channel receptors.

Authors: Chen, Zheng

Year: 2023

Venue: University of Sydney

DOI: https://hdl.handle.net/2123/31946

Thesis The Pros and Cons of Backbone Flexibility in Molecular Dynamics Docking of Protein Complexes

Faruk, Nabil F. · 2022 · University of Chicago - Knowledge@UChicago · DOI

Full title: The Pros and Cons of Backbone Flexibility in Molecular Dynamics Docking of Protein Complexes

Authors: Faruk, Nabil F.

Year: 2022

Venue: University of Chicago - Knowledge@UChicago

DOI: https://knowledge.uchicago.edu/record/3630/files/Faruk_uchicago_0330D_16135.pdf

Thesis Macromolecular Structure Prediction to Guide Studies of RNA Virus Proteins

Caballes, Raphael · 2025 · UNSW Sydney · DOI

Full title: Macromolecular Structure Prediction to Guide Studies of RNA Virus Proteins

Authors: Caballes, Raphael

Year: 2025

Venue: UNSW Sydney

DOI: http://hdl.handle.net/1959.4/105640

Thesis Towards determination of binding poses of novel HIV-1 reverse transcriptase ligands using in silico methods

Dupree, Tom · 2018 · UNSW Sydney · DOI

Full title: Towards determination of binding poses of novel HIV-1 reverse transcriptase ligands using in silico methods

Authors: Dupree, Tom

Year: 2018

Venue: UNSW Sydney

DOI: http://hdl.handle.net/1959.4/60489

Thesis Artificial Intelligence and High-Performance Computing for Accelerating Structure-Based Drug Discovery

Clyde, Austin Robert · 2022 · University of Chicago - Knowledge@UChicago · DOI

Full title: Artificial Intelligence and High-Performance Computing for Accelerating Structure-Based Drug Discovery

Authors: Clyde, Austin Robert

Year: 2022

Venue: University of Chicago - Knowledge@UChicago

DOI: https://knowledge.uchicago.edu/record/5266/files/Clyde_uchicago_0330D_16709.pdf

Thesis Molecular models of NS3 protease variants of the Hepatitis C virus

da Silveira, NJF; Arcuri, H. A.; Bonalumi, C. E. et al. · 2014 · Universidade Estadual Paulista (UNESP) · DOI

Full title: Molecular models of NS3 protease variants of the Hepatitis C virus

Authors: da Silveira, NJF; Arcuri, H. A.; Bonalumi, C. E.; de Souza, F. P.; Mello, IMVGC; Rahal, Paula [UNESP]; Pinho, JRR; de Azevedo, W. F.

Year: 2014

Venue: Universidade Estadual Paulista (UNESP)

DOI: http://dx.doi.org/10.1186/1472-6807-5-1

Thesis Natural Compounds as Non-Nucleoside Inhibitors of Zika Virus Polymerase through Integration of In Silico and In Vitro Approaches

Ramos, Paulo Ricardo Pimenta da Silva; Mottin, Melina; Lima, Caroline Sprengel [UNESP] et al. · 2023 · Universidade Estadual Paulista (UNESP) · DOI

Full title: Natural Compounds as Non-Nucleoside Inhibitors of Zika Virus Polymerase through Integration of In Silico and In Vitro Approaches

Authors: Ramos, Paulo Ricardo Pimenta da Silva; Mottin, Melina; Lima, Caroline Sprengel [UNESP]; Assis, Letícia R. [UNESP]; de Oliveira, Ketllyn Zagato; Mesquita, Nathalya Cristina de Moraes Roso; Cassani, Natasha Marques; Santos, Igor Andrade; Borba, Joyce Villa Verde Bastos; Fiaia Costa, Vinícius Alexandre; Neves, Bruno Junior; Guido, Rafael Victorio Carvalho; Oliva, Glaucius; Jardim, Ana Carolina Gomes; Regasini, Luis Octávio [UNESP]; Andrade, Carolina Horta

Year: 2023

Venue: Universidade Estadual Paulista (UNESP)

DOI: http://dx.doi.org/10.3390/ph15121493

Thesis The impact of protein structure and sequence similarity on the accuracy of machine-learning scoring functions for binding affinity prediction

Li, Hongjian; Peng, Jiangjun; Leung, Yee et al. · 2024 · Imperial College London · DOI

Full title: The impact of protein structure and sequence similarity on the accuracy of machine-learning scoring functions for binding affinity prediction

Authors: Li, Hongjian; Peng, Jiangjun; Leung, Yee; Leung, Kwong-Sak; Wong, Man-Hon; Lu, Gang; Ballester, Pedro

Year: 2024

Venue: Imperial College London

DOI: https://www.mdpi.com/2218-273X/8/1/12

Thesis Performance of machine-learning scoring functions in structure-based virtual screening

Wójcikowski, Maciej; Ballester, Pedro J; Siedlecki, Pawel · 2024 · Imperial College London · DOI

Full title: Performance of machine-learning scoring functions in structure-based virtual screening

Authors: Wójcikowski, Maciej; Ballester, Pedro J; Siedlecki, Pawel

Year: 2024

Venue: Imperial College London

DOI: https://doi.org/10.1038/srep46710

Thesis Homology modeling informs ligand discovery for the glutamine transporter ASCT2

Garibsingh, RAA; Otte, NJ; Ndaru, E et al. · 2018 · UNSW Sydney · DOI

Full title: Homology modeling informs ligand discovery for the glutamine transporter ASCT2

Authors: Garibsingh, RAA; Otte, NJ; Ndaru, E; Colas, C; Grewer, C; Holst, J ; https://orcid.org/0000-0002-0377-9318; Schlessinger, A

Year: 2018

Venue: UNSW Sydney

DOI: http://hdl.handle.net/1959.4/unsworks_82529

Thesis B-Cell Epitope Prediction for Improved Antibody Docking

Rontogiannis, Aristofanis · 2023 · Massachusetts Institute of Technology (MIT) · DOI

Full title: B-Cell Epitope Prediction for Improved Antibody Docking

Authors: Rontogiannis, Aristofanis

Year: 2023

Venue: Massachusetts Institute of Technology (MIT)

DOI: https://hdl.handle.net/1721.1/150148

Thesis Biological vs. Crystallographic protein interfaces: An overview of computational approaches for their classification

Elez, Katarina; Bonvin, Alexandre M.J.J.; Vangone, Anna · 2020 · Utrecht University · DOI

Full title: Biological vs. Crystallographic protein interfaces: An overview of computational approaches for their classification

Authors: Elez, Katarina; Bonvin, Alexandre M.J.J.; Vangone, Anna

Year: 2020

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/396135

Thesis Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes.

Mikolajek, Halina; Weckener, Miriam; Brotzakis, Z Faidon et al. · 2022 · University of Cambridge · DOI

Full title: Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes.

Authors: Mikolajek, Halina; Weckener, Miriam; Brotzakis, Z Faidon; Huo, Jiandong; Dalietou, Evmorfia V; Le Bas, Audrey; Sormanni, Pietro; Harrison, Peter J; Ward, Philip N; Truong, Steven; Moynie, Lucile; Clare, Daniel K; Dumoux, Maud; Dormon, Joshua; Norman, Chelsea; Hussain, Naveed; Vogirala, Vinod; Owens, Raymond J; Vendruscolo, Michele; Naismith, James H

Year: 2022

Venue: University of Cambridge

DOI: https://www.repository.cam.ac.uk/handle/1810/340308

Thesis MolScore: a scoring, evaluation and benchmarking framework for generative models in de novo drug design

Thomas, Morgan; O'Boyle, Noel M; Bender, Andreas et al. · 2024 · University of Cambridge · DOI

Full title: MolScore: a scoring, evaluation and benchmarking framework for generative models in de novo drug design

Authors: Thomas, Morgan; O'Boyle, Noel M; Bender, Andreas; De Graaf, Chris

Year: 2024

Venue: University of Cambridge

DOI: https://www.repository.cam.ac.uk/handle/1810/369087

Thesis Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

Lensink, Marc F.; Velankar, Sameer; Kryshtafovych, Andriy et al. · 2016 · Utrecht University · DOI

Full title: Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

Authors: Lensink, Marc F.; Velankar, Sameer; Kryshtafovych, Andriy; Huang, Shen You; Schneidman-Duhovny, Dina; Sali, Andrej; Segura, Joan; Fernandez-Fuentes, Narcis; Viswanath, Shruthi; Elber, Ron; Grudinin, Sergei; Popov, Petr; Neveu, Emilie; Lee, Hasup; Baek, Minkyung; Park, Sangwoo; Heo, Lim; Rie Lee, Gyu; Seok, Chaok; Qin, Sanbo; Zhou, Huan Xiang; Ritchie, David W.; Maigret, Bernard; Devignes, Marie Dominique; Ghoorah, Anisah; Torchala, Mieczyslaw; Chaleil, Raphaël A G; Bates, Paul A.; Ben-Zeev, Efrat; Eisenstein, Miriam; Negi, Surendra S.; Weng, Zhiping; Vreven, Thom; Pierce, Brian G.; Borrman, Tyler M.; Yu, Jinchao; Ochsenbein, Françoise; Guerois, Raphaël; Vangone, Anna; Garcia Lopes Maia Rodrigues, João; van Zundert, Gydo; Nellen, Mehdi; Xue, Li; Karaca, Ezgi; Melquiond, Adrien S J; Visscher, Koen; Kastritis, Panagiotis L.; Bonvin, Alexandre M J J; Xu, Xianjin; Qiu, Liming; Yan, Chengfei; Li, Jilong; Ma, Zhiwei; Cheng, Jianlin; Zou, Xiaoqin; Shen, Yang; Peterson, Lenna X.; Kim, Hyung Rae; Roy, Amit; Han, Xusi; Esquivel-Rodriguez, Juan; Kihara, Daisuke; Yu, Xiaofeng; Bruce, Neil J.; Fuller, Jonathan C.; Wade, Rebecca C.; Anishchenko, Ivan; Kundrotas, Petras J.; Vakser, Ilya A.; Imai, Kenichiro; Yamada, Kazunori; Oda, Toshiyuki; Nakamura, Tsukasa; Tomii, Kentaro; Pallara, Chiara; Romero-Durana, Miguel; Jiménez-García, Brian; Moal, Iain H.; Férnandez-Recio, Juan; Joung, Jong Young; Kim, Jong Yun; Joo, Keehyoung; Lee, Jooyoung; Kozakov, Dima; Vajda, Sandor; Mottarella, Scott; Hall, David R.; Beglov, Dmitri; Mamonov, Artem; Xia, Bing; Bohnuud, Tanggis; Del Carpio, Carlos A.; Ichiishi, Eichiro; Marze, Nicholas; Kuroda, Daisuke; Roy Burman, Shourya S.; Gray, Jeffrey J.; Chermak, Edrisse; Cavallo, Luigi; Oliva, Romina; Tovchigrechko, Andrey; Wodak, Shoshana J.

Year: 2016

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/337451

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Paper AI-Enhanced Adaptive Virtual Screening Platform Enabling Exploration of 69 Billion Molecules Discovers Structurally Validated FSP1 Inhibitors

Gorgulla, Christoph; Nigam, AkshatKumar; Koop, Matt et al. · 2023 · DOI

Full title: AI-Enhanced Adaptive Virtual Screening Platform Enabling Exploration of 69 Billion Molecules Discovers Structurally Validated FSP1 Inhibitors

Authors: Gorgulla, Christoph; Nigam, AkshatKumar; Koop, Matt; Çınaroğlu, Süleyman Selim; Secker, Christopher; Haddadnia, Mohammad; Abhishek, Kumar; Malets, Yehor S.; Hasson, Alexander; Li, M; Tang, Ming; Levin‐Konigsberg, Roni; Radchenko, Dmitry; Kumar, Aditya; Gehev, Minko; Aquilanti, Pierre-Yves; Gabb, Henry A.; Alhossary, Amr; Wagner, Gerhard; Aspuru‐Guzik, Alán; Moroz, Yurii S.; Fackeldey, Konstantin; Arthanari, Haribabu; Choi, Eun-Bee; Shapiro, Geoffrey; Cox, Huel; Sebastian, Luke; Braithwaite, Chelsea; Bashyal, Puspalata; Radchenko, Dmytro S.; Kumar, Aditya; Gehev, Minko; Aquilanti, Pierre-Yves; Gabb, Henry; Alhossary, Amr; Wagner, Gerhard; Aspuru-Guzik, Alan; Moroz, Yurii S.; Kalodimos, Charalampos G.; Fackeldey, Konstantin; Mattevi, Andrea; Arthanari, Haribabu

Year: 2023

DOI: https://doi.org/10.1101/2023.04.25.537981

Paper Fully flexible molecular alignment enables accurate ligand structure modelling

Wang, Zhihao; Zhou, Fan; Wang, Zechen et al. · 2023 · DOI

Full title: Fully flexible molecular alignment enables accurate ligand structure modelling

Authors: Wang, Zhihao; Zhou, Fan; Wang, Zechen; Li, Yongqiang; Wang, Sheng; Zheng, Liangzhen; Li, Weifeng; Peng, Xiangda

Year: 2023

DOI: https://doi.org/10.1101/2023.12.17.572051

Paper Simpatico: accurate and ultra-fast virtual drug screening with atomic embeddings

Gaiser, Jeremiah; Wheeler, Travis J. · 2025 · DOI

Full title: Simpatico: accurate and ultra-fast virtual drug screening with atomic embeddings

Authors: Gaiser, Jeremiah; Wheeler, Travis J.

Year: 2025

DOI: https://doi.org/10.1101/2025.06.08.658499

Paper Simulation and Machine Learning Methods for Ion-Channel Structure Determination, Mechanistic Studies and Drug Design

Zhu, Zhengdan; Deng, Zhenfeng; Wang, Qinrui et al. · 2022 · Frontiers in Pharmacology · DOI

Full title: Simulation and Machine Learning Methods for Ion-Channel Structure Determination, Mechanistic Studies and Drug Design

Authors: Zhu, Zhengdan; Deng, Zhenfeng; Wang, Qinrui; Wang, Yuhang; Zhang, Duo; Xu, Ruihan; Guo, Lvjun; Wen, Han

Year: 2022

Venue: Frontiers in Pharmacology

DOI: https://doi.org/10.3389/fphar.2022.939555

Paper Searching for New Z-DNA/Z-RNA Binding Proteins Based on Structural Similarity to Experimentally Validated Zα Domain

Bartas, Martin; Slychko, Kristyna; Brázda, Václav et al. · 2022 · International Journal of Molecular Sciences · DOI

Full title: Searching for New Z-DNA/Z-RNA Binding Proteins Based on Structural Similarity to Experimentally Validated Zα Domain

Authors: Bartas, Martin; Slychko, Kristyna; Brázda, Václav; Červeň, Jiří; Beaudoin, Christopher A.; Blundell, Tom L.; Pečínka, Petr

Year: 2022

Venue: International Journal of Molecular Sciences

DOI: https://doi.org/10.3390/ijms23020768

Paper Computational Approaches Drive Developments in Immune-Oncology Therapies for PD-1/PD-L1 Immune Checkpoint Inhibitors

Sobral, Patrícia; Luz, Vanessa C. C.; Almeida, João M. G. C. F. et al. · 2023 · International Journal of Molecular Sciences · DOI

Full title: Computational Approaches Drive Developments in Immune-Oncology Therapies for PD-1/PD-L1 Immune Checkpoint Inhibitors

Authors: Sobral, Patrícia; Luz, Vanessa C. C.; Almeida, João M. G. C. F.; Videira, Paula A.; Pereira, Florbela

Year: 2023

Venue: International Journal of Molecular Sciences

DOI: https://doi.org/10.3390/ijms24065908

Paper Therapeutic Potential of Natural Products in the Treatment of Schistosomiasis

Azevedo, Carine Machado; Meira, Cássio Santana; Silva, Jaqueline et al. · 2023 · Molecules · DOI

Full title: Therapeutic Potential of Natural Products in the Treatment of Schistosomiasis

Authors: Azevedo, Carine Machado; Meira, Cássio Santana; Silva, Jaqueline; Moura, Danielle Maria Nascimento; Oliveira, Sheilla Andrade de; Costa, Cícero Jádson da; Santos, Emanuelle de Souza; Soares, Milena Botelho Pereira

Year: 2023

Venue: Molecules

DOI: https://doi.org/10.3390/molecules28196807

Paper The Prediction of LptA and LptC Protein–Protein Interactions and Virtual Screening for Potential Inhibitors

Ren, Yixin; Dong, Wenting; Li, Yan et al. · 2024 · Molecules · DOI

Full title: The Prediction of LptA and LptC Protein–Protein Interactions and Virtual Screening for Potential Inhibitors

Authors: Ren, Yixin; Dong, Wenting; Li, Yan; Cao, Weiting; Xiao, Zengshuo; Zhou, Ying; Teng, Yun; You, Xuefu; Yang, Xinyi; Huang, Huoqiang; Wang, Hao

Year: 2024

Venue: Molecules

DOI: https://doi.org/10.3390/molecules29081827

Paper Riluzole, a Derivative of Benzothiazole as a Potential Anti-Amoebic Agent against Entamoeba histolytica

Velásquez-Torres, Maritza; Trujillo‐Ferrara, José G.; Godínez‐Victoria, Marycarmen et al. · 2023 · Pharmaceuticals · DOI

Full title: Riluzole, a Derivative of Benzothiazole as a Potential Anti-Amoebic Agent against Entamoeba histolytica

Authors: Velásquez-Torres, Maritza; Trujillo‐Ferrara, José G.; Godínez‐Victoria, Marycarmen; Jarillo‐Luna, Rosa Adriana; Tsutsumi, Vı́ctor; Sánchez‐Monroy, Virginia; Posadas‐Mondragón, Araceli; Cuevas‐Hernández, Roberto I.; Santiago-Cruz, José Angel; Pacheco‐Yépez, Judith

Year: 2023

Venue: Pharmaceuticals

DOI: https://doi.org/10.3390/ph16060896

Paper Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles

Fukunishi, Yoshifumi; Higo, Junichi; Kasahara, Kota · 2022 · Biophysical Reviews · DOI

Full title: Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles

Authors: Fukunishi, Yoshifumi; Higo, Junichi; Kasahara, Kota

Year: 2022

Venue: Biophysical Reviews

DOI: https://doi.org/10.1007/s12551-022-01015-8

Paper Navigating the landscape of enzyme design: from molecular simulations to machine learning

Zhou, Jiahui; Huang, Meilan · 2024 · Chemical Society Reviews · DOI

Full title: Navigating the landscape of enzyme design: from molecular simulations to machine learning

Authors: Zhou, Jiahui; Huang, Meilan

Year: 2024

Venue: Chemical Society Reviews

DOI: https://doi.org/10.1039/d4cs00196f

Paper Molecular determinants of antagonist interactions with chemokine receptors CCR2 and CCR5

Dawson, John R.D.; Wadman, Grant M.; Zhang, Penglie et al. · 2023 · DOI

Full title: Molecular determinants of antagonist interactions with chemokine receptors CCR2 and CCR5

Authors: Dawson, John R.D.; Wadman, Grant M.; Zhang, Penglie; Tebben, Andrew J.; Carter, Percy H.; Gu, Siyi; Shroka, Thomas M.; Borrega‐Román, Leire; Salanga, Catherina L.; Handel, Tracy M.; Kufareva, Irina

Year: 2023

DOI: https://doi.org/10.1101/2023.11.15.567150

Paper Fast and accurate modeling and design of antibody-antigen complex using tFold

Wu, Fandi; Zhao, Yu; Wu, Jiaxiang et al. · 2024 · DOI

Full title: Fast and accurate modeling and design of antibody-antigen complex using tFold

Authors: Wu, Fandi; Zhao, Yu; Wu, Jiaxiang; Jiang, Biaobin; He, Bing; Huang, Long-Kai; Qin, Chenchen; Yang, Fan; Huang, Ningqiao; Xiao, Yang; Wang, Rubo; Jia, Huaxian; Rong, Yu; Liu, Yuyi; Lai, Houtim; Xu, Tingyang; Liu, Wei; Zhao, Peilin; Yao, Jianhua

Year: 2024

DOI: https://doi.org/10.1101/2024.02.05.578892

Paper Towards a Truly General Intermolecular Binding Affinity Calculator for Drug Discovery & Design

Li, Wei; Vottevor, Gary · 2023 · Preprints.org · DOI

Full title: Towards a Truly General Intermolecular Binding Affinity Calculator for Drug Discovery & Design

Authors: Li, Wei; Vottevor, Gary

Year: 2023

Venue: Preprints.org

DOI: https://doi.org/10.20944/preprints202208.0213.v2

Paper Protein Science Meets Artificial Intelligence: A Systematic Review and a Biochemical Meta-Analysis of an Inter-Field

Villalobos-Alva, Jalil; Ochoa-Toledo, Luis; Villalobos-Alva, Mario Javier et al. · 2022 · Frontiers in Bioengineering and Biotechnology · DOI

Full title: Protein Science Meets Artificial Intelligence: A Systematic Review and a Biochemical Meta-Analysis of an Inter-Field

Authors: Villalobos-Alva, Jalil; Ochoa-Toledo, Luis; Villalobos-Alva, Mario Javier; Aliseda, Atocha; Pérez‐Escamirosa, Fernando; Altamirano-Bustamante, Nelly; Ochoa-Fernández, Francine; Zamora-Solís, Ricardo; Villalobos-Alva, Sebastián; Revilla, M.; Kemper-Valverde, Nicolás C.; Altamirano‐Bustamante, Myriam M.

Year: 2022

Venue: Frontiers in Bioengineering and Biotechnology

DOI: https://doi.org/10.3389/fbioe.2022.788300

Paper Protein Function Analysis through Machine Learning

Avery, Chris; Patterson, Julie A.; Grear, Tyler et al. · 2022 · Biomolecules · DOI

Full title: Protein Function Analysis through Machine Learning

Authors: Avery, Chris; Patterson, Julie A.; Grear, Tyler; Frater, Theodore D.; Jacobs, Donald J.

Year: 2022

Venue: Biomolecules

DOI: https://doi.org/10.3390/biom12091246

Paper Comprehensive Survey of Recent Drug Discovery Using Deep Learning

Kim, Jintae; Park, Sera; Min, Dongbo et al. · 2021 · International Journal of Molecular Sciences · DOI

Full title: Comprehensive Survey of Recent Drug Discovery Using Deep Learning

Authors: Kim, Jintae; Park, Sera; Min, Dongbo; Kim, Wankyu

Year: 2021

Venue: International Journal of Molecular Sciences

DOI: https://doi.org/10.3390/ijms22189983

Paper Virtual Screening of Peptide Libraries: The Search for Peptide-Based Therapeutics Using Computational Tools

Vincenzi, Marian; Mercurio, Flavia Anna; Leone, Marilisa · 2024 · International Journal of Molecular Sciences · DOI

Full title: Virtual Screening of Peptide Libraries: The Search for Peptide-Based Therapeutics Using Computational Tools

Authors: Vincenzi, Marian; Mercurio, Flavia Anna; Leone, Marilisa

Year: 2024

Venue: International Journal of Molecular Sciences

DOI: https://doi.org/10.3390/ijms25031798

Paper Emerging Pharmacotherapeutic Strategies to Overcome Undruggable Proteins in Cancer

Lu, Yuqing; Yang, Yuewen; Zhu, Guanghao et al. · 2023 · International Journal of Biological Sciences · DOI

Full title: Emerging Pharmacotherapeutic Strategies to Overcome Undruggable Proteins in Cancer

Authors: Lu, Yuqing; Yang, Yuewen; Zhu, Guanghao; Zeng, Hairong; Fan, Yi‐Ming; Guo, Fujia; Xu, Dongshu; Wang, Boya; Chen, Dapeng; Ge, Guang‐Bo

Year: 2023

Venue: International Journal of Biological Sciences

DOI: https://doi.org/10.7150/ijbs.83026

Paper Computer-Aided Drug Design towards New Psychotropic and Neurological Drugs

Dorahy, Georgia; Chen, Zheng; Balle, Thomas · 2023 · Molecules · DOI

Full title: Computer-Aided Drug Design towards New Psychotropic and Neurological Drugs

Authors: Dorahy, Georgia; Chen, Zheng; Balle, Thomas

Year: 2023

Venue: Molecules

DOI: https://doi.org/10.3390/molecules28031324

Paper Opportunities and Challenges for In Silico Drug Discovery at Delta Opioid Receptors

Meqbil, Yazan J.; Rijn, Richard M. van · 2022 · Pharmaceuticals · DOI

Full title: Opportunities and Challenges for In Silico Drug Discovery at Delta Opioid Receptors

Authors: Meqbil, Yazan J.; Rijn, Richard M. van

Year: 2022

Venue: Pharmaceuticals

DOI: https://doi.org/10.3390/ph15070873

Paper Recent Progress of Protein Tertiary Structure Prediction

Wuyun, Qiqige; Chen, Yihan; Shen, Yifeng et al. · 2024 · Molecules · DOI

Full title: Recent Progress of Protein Tertiary Structure Prediction

Authors: Wuyun, Qiqige; Chen, Yihan; Shen, Yifeng; Cao, Yang; Hu, Gang; Cui, Wei; Gao, Jianzhao; Zheng, Wei

Year: 2024

Venue: Molecules

DOI: https://doi.org/10.3390/molecules29040832

Paper Quality Assessment of Selected Protein Structures Derived from Homology Modeling and AlphaFold

Binbay, Furkan Ayberk; Rathod, Darshan; George, Ajay Abisheck Paul et al. · 2023 · Pharmaceuticals · DOI

Full title: Quality Assessment of Selected Protein Structures Derived from Homology Modeling and AlphaFold

Authors: Binbay, Furkan Ayberk; Rathod, Darshan; George, Ajay Abisheck Paul; Imhof, Diana

Year: 2023

Venue: Pharmaceuticals

DOI: https://doi.org/10.3390/ph16121662

Paper Computer-Aided Drug Design and Drug Discovery: A Prospective Analysis

Niazi, Sarfaraz K.; Mariam, Zamara · 2023 · Pharmaceuticals · DOI

Full title: Computer-Aided Drug Design and Drug Discovery: A Prospective Analysis

Authors: Niazi, Sarfaraz K.; Mariam, Zamara

Year: 2023

Venue: Pharmaceuticals

DOI: https://doi.org/10.3390/ph17010022

Paper A Comprehensive Computational Insight into the PD-L1 Binding to PD-1 and Small Molecules

Fantacuzzi, Marialuigia; Paciotti, Roberto; Agamennone, Mariangela · 2024 · Pharmaceuticals · DOI

Full title: A Comprehensive Computational Insight into the PD-L1 Binding to PD-1 and Small Molecules

Authors: Fantacuzzi, Marialuigia; Paciotti, Roberto; Agamennone, Mariangela

Year: 2024

Venue: Pharmaceuticals

DOI: https://doi.org/10.3390/ph17030316

Paper Novel computational pipelines in antiviral structure‑based drug design (Review)

Diakou, Io; Papakonstantinou, Eleni; Papageorgiou, Louis et al. · 2022 · Biomedical Reports · DOI

Full title: Novel computational pipelines in antiviral structure‑based drug design (Review)

Authors: Diakou, Io; Papakonstantinou, Eleni; Papageorgiou, Louis; Pierouli, Katerina; Dragoumani, Konstantina; Spandidos, Demetrios��; Bacopoulou, Flora; Chrousos, George P.; Eliopoulos, Elias; Vlachakis, Dimitriοs

Year: 2022

Venue: Biomedical Reports

DOI: https://doi.org/10.3892/br.2022.1580

Paper A Shortcut from Genome to Drug: The Employment of Bioinformatic Tools to Find New Targets for Gastric Cancer Treatment

Brito, Daiane Maria da Silva; Lima, Odnan G.; Mesquita, Felipe Pantoja et al. · 2023 · Pharmaceutics · DOI

Full title: A Shortcut from Genome to Drug: The Employment of Bioinformatic Tools to Find New Targets for Gastric Cancer Treatment

Authors: Brito, Daiane Maria da Silva; Lima, Odnan G.; Mesquita, Felipe Pantoja; Silva, Emerson Lucena da; Moraes, Maria Elisabete Amaral de; Burbano, Rommel Mário Rodríguez; Montenegro, Raquel Carvalho; Souza, Pedro Filho Noronha

Year: 2023

Venue: Pharmaceutics

DOI: https://doi.org/10.3390/pharmaceutics15092303

Paper ML-Driven Approach to Discovery of Peptide-Based BACE1 Inhibitors

Chen, Nicholas · 2025 · International journal of high school research · DOI

Full title: ML-Driven Approach to Discovery of Peptide-Based BACE1 Inhibitors

Authors: Chen, Nicholas

Year: 2025

Venue: International journal of high school research

DOI: https://doi.org/10.36838/v7i4.5

Paper The Recent Advances in the Approach of Artificial Intelligencetowards Medicine Discovery

L.Choundhe, Puja L.Choundhe Puja, A.Dhoke, Payal A.Dhoke Payal, Deshpande, Rutuja, S.Dahekar, Praktan S.Dahekar Praktan, Dangare, Tushar C. Dangare Tushar C. · 2025 · International Journal of Pharmaceutical Research and Applications · DOI

Full title: The Recent Advances in the Approach of Artificial Intelligencetowards Medicine Discovery

Authors: L.Choundhe, Puja L.Choundhe Puja, A.Dhoke, Payal A.Dhoke Payal, Deshpande, Rutuja, S.Dahekar, Praktan S.Dahekar Praktan, Dangare, Tushar C. Dangare Tushar C.

Year: 2025

Venue: International Journal of Pharmaceutical Research and Applications

DOI: https://doi.org/10.35629/4494-10033442

Paper FABind+: Enhancing Molecular Docking through Improved Pocket Prediction and Pose Generation

Gao, Kaiyuan; Pei, Qizhi; Jinhua, Zhu et al. · 2024 · arXiv (Cornell University) · DOI

Full title: FABind+: Enhancing Molecular Docking through Improved Pocket Prediction and Pose Generation

Authors: Gao, Kaiyuan; Pei, Qizhi; Jinhua, Zhu; Qin, Tao; He, Kun; Wu, Lijun

Year: 2024

Venue: arXiv (Cornell University)

DOI: https://doi.org/10.48550/arxiv.2403.20261

Paper EquiCPI: SE(3)-Equivariant Geometric Deep Learning for Structure-Aware Prediction of Compound-Protein Interactions

Nguyen, Ngoc-Quang · 2025 · arXiv (Cornell University) · DOI

Full title: EquiCPI: SE(3)-Equivariant Geometric Deep Learning for Structure-Aware Prediction of Compound-Protein Interactions

Authors: Nguyen, Ngoc-Quang

Year: 2025

Venue: arXiv (Cornell University)

DOI: https://doi.org/10.48550/arxiv.2504.04654

Paper Enhancing Ligand Pose Sampling for Molecular Docking

Patricia Suriana; R. Dror · 2023 · arXiv.org · DOI

Full title: Enhancing Ligand Pose Sampling for Molecular Docking

Authors: Patricia Suriana; R. Dror

Year: 2023

Venue: arXiv.org

DOI: https://doi.org/10.48550/arxiv.2312.00191

Paper AI-Driven Molecular Design and Screening for Drug Discovery

G, Tani Carmel Raj T, Shastry, K. Aditya · 2025 · INTERANTIONAL JOURNAL OF SCIENTIFIC RESEARCH IN ENGINEERING AND MANAGEMENT · DOI

Full title: AI-Driven Molecular Design and Screening for Drug Discovery

Authors: G, Tani Carmel Raj T, Shastry, K. Aditya

Year: 2025

Venue: INTERANTIONAL JOURNAL OF SCIENTIFIC RESEARCH IN ENGINEERING AND MANAGEMENT

DOI: https://doi.org/10.55041/ijsrem52104

Paper Artificial Intelligence and Machine Learning Approaches for Target-Based Drug Discovery: A Focus on GPCR-Ligand Interactions

Otun, Martins · 2025 · Journal of applied science and environmental management · DOI

Full title: Artificial Intelligence and Machine Learning Approaches for Target-Based Drug Discovery: A Focus on GPCR-Ligand Interactions

Authors: Otun, Martins

Year: 2025

Venue: Journal of applied science and environmental management

DOI: https://doi.org/10.4314/jasem.v29i3.7

Paper EQUIBIND: A geometric deep learning-based protein-ligand binding prediction method

Li, Yuze; Li, Li; Wang, Shuang et al. · 2023 · Drug Discoveries & Therapeutics · DOI

Full title: EQUIBIND: A geometric deep learning-based protein-ligand binding prediction method

Authors: Li, Yuze; Li, Li; Wang, Shuang; Tang, Xiaowen

Year: 2023

Venue: Drug Discoveries & Therapeutics

DOI: https://doi.org/10.5582/ddt.2023.01063

Paper The Role of Artificial Intelligence in Drug Discovery

Jadge, Sanika Kamble*, Sneha Wavdane, Vishal Mote, Dhanraj · 2025 · Zenodo (CERN European Organization for Nuclear Research) · DOI

Full title: The Role of Artificial Intelligence in Drug Discovery

Authors: Jadge, Sanika Kamble*, Sneha Wavdane, Vishal Mote, Dhanraj

Year: 2025

Venue: Zenodo (CERN European Organization for Nuclear Research)

DOI: https://doi.org/10.5281/zenodo.17840354

Paper Machine Learning-Driven Anticancer Drug Discovery: From Virtual Screening to Preclinical Validation

Wang, Yiyan · 2025 · Advances in Engineering Technology Research · DOI

Full title: Machine Learning-Driven Anticancer Drug Discovery: From Virtual Screening to Preclinical Validation

Authors: Wang, Yiyan

Year: 2025

Venue: Advances in Engineering Technology Research

DOI: https://doi.org/10.56028/aetr.14.1.1503.2025

Paper Protein Structure Prediction Tools and Computational Approaches

Garavano, Natalia, Sadosky, Francisca, Bulgheroni, Facundo · 2023 · Fusion of Multidisciplinary Research An International Journal · DOI

Full title: Protein Structure Prediction Tools and Computational Approaches

Authors: Garavano, Natalia, Sadosky, Francisca, Bulgheroni, Facundo

Year: 2023

Venue: Fusion of Multidisciplinary Research An International Journal

DOI: https://doi.org/10.63995/mwcu4408

Paper FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction.

Morehead, Alex, Cheng, Jianlin · 2025 · PubMed

Full title: FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction.

Authors: Morehead, Alex, Cheng, Jianlin

Year: 2025

Venue: PubMed

Paper The Role of Artificial Intelligence in Drug Discovery

Jadge, Sanika Kamble*, Sneha Wavdane, Vishal Mote, Dhanraj · 2025 · Zenodo (CERN European Organization for Nuclear Research) · DOI

Full title: The Role of Artificial Intelligence in Drug Discovery

Authors: Jadge, Sanika Kamble*, Sneha Wavdane, Vishal Mote, Dhanraj

Year: 2025

Venue: Zenodo (CERN European Organization for Nuclear Research)

DOI: https://doi.org/10.5281/zenodo.17840353

Paper Structure-guided computational insecticide discovery targeting β-N-acetyl-D-hexosaminidase of Ostrinia furnacalis

Tahir, Adeena, Siddiqi, Abdul Rauf, Maryam, Arooma, Vedithi, Sundeep Chaitanya, Blundell, Tom L. · 2023 · Figshare · DOI

Full title: Structure-guided computational insecticide discovery targeting β-N-acetyl-D-hexosaminidase of Ostrinia furnacalis

Authors: Tahir, Adeena, Siddiqi, Abdul Rauf, Maryam, Arooma, Vedithi, Sundeep Chaitanya, Blundell, Tom L.

Year: 2023

Venue: Figshare

DOI: https://doi.org/10.6084/m9.figshare.24278140

Paper Role of Chemoinformatics and Machine Learning in Drug Repurposing

Sirci, Francesco; Güney, Emre · 2025 · Drug repurposing · DOI

Full title: Role of Chemoinformatics and Machine Learning in Drug Repurposing

Authors: Sirci, Francesco; Güney, Emre

Year: 2025

Venue: Drug repurposing

DOI: https://doi.org/10.58647/drugrepo.25.1.0005

Paper Fundamentals of Molecular Docking and Comparative Analysis of Protein–Small-Molecule Docking Approaches

Maden, Sefika Feyza; Sezer, Selin; Acuner, Saliha Ece · 2022 · Biomedical engineering · DOI

Full title: Fundamentals of Molecular Docking and Comparative Analysis of Protein–Small-Molecule Docking Approaches

Authors: Maden, Sefika Feyza; Sezer, Selin; Acuner, Saliha Ece

Year: 2022

Venue: Biomedical engineering

DOI: https://doi.org/10.5772/intechopen.105815

Paper Structure-guided computational insecticide discovery targeting β-N-acetyl-D-hexosaminidase of Ostrinia furnacalis

Satti, Adeena Tahir, Siddiqi, Abdul Rauf, Maryam, Arooma, Vedithi, Sundeep Chaitanya, Blundell, Tom L. · 2023 · Figshare · DOI

Full title: Structure-guided computational insecticide discovery targeting β-N-acetyl-D-hexosaminidase of Ostrinia furnacalis

Authors: Satti, Adeena Tahir, Siddiqi, Abdul Rauf, Maryam, Arooma, Vedithi, Sundeep Chaitanya, Blundell, Tom L.

Year: 2023

Venue: Figshare

DOI: https://doi.org/10.6084/m9.figshare.24278140.v1

Paper RAPID-Net: Accurate Pocket Identification for Binding-Site-Agnostic Docking.

Balytskyi, Yaroslav; Hubenko, Inna; Balytska, Alina et al. · 2025 · Journal of chemical information and modeling · DOI

Full title: RAPID-Net: Accurate Pocket Identification for Binding-Site-Agnostic Docking.

Authors: Balytskyi, Yaroslav; Hubenko, Inna; Balytska, Alina; Kelly, Christopher V

Year: 2025

Venue: Journal of chemical information and modeling

DOI: https://doi.org/10.1021/acs.jcim.5c01744

Paper Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field

Schlick, Tamar; Portillo‐Ledesma, Stephanie; Myers, Christopher G. et al. · 2021 · Annual Review of Biophysics · DOI

Full title: Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field

Authors: Schlick, Tamar; Portillo‐Ledesma, Stephanie; Myers, Christopher G.; Beljak, Lauren; Chen, Justin; Dakhel, Sami; Darling, D.H.; Ghosh, Sayak; Hall, Joseph W.; Jan, Mikaeel; Liang, Emily C.; Saju, Sera; Vohr, Mackenzie; Wu, Chris; Xu, Yifan; Xue, Eva

Year: 2021

Venue: Annual Review of Biophysics

DOI: https://doi.org/10.1146/annurev-biophys-091720-102019

Paper Exploration and augmentation of pharmacological space via adversarial auto-encoder model for facilitating kinase-centric drug development

Bai, Xinyu, Yin, Yuxin · 2021 · Journal of Cheminformatics · DOI

Full title: Exploration and augmentation of pharmacological space via adversarial auto-encoder model for facilitating kinase-centric drug development

Authors: Bai, Xinyu, Yin, Yuxin

Year: 2021

Venue: Journal of Cheminformatics

DOI: https://doi.org/10.1186/s13321-021-00574-4

Paper Identification of Potential WSB1 Inhibitors by AlphaFold Modeling, Virtual Screening, and Molecular Dynamics Simulation Studies.

Weng, Ye; Pan, Chenghao; Shen, Zheyuan et al. · 2022 · Evidence-based complementary and alternative medicine : eCAM · DOI

Full title: Identification of Potential WSB1 Inhibitors by AlphaFold Modeling, Virtual Screening, and Molecular Dynamics Simulation Studies.

Authors: Weng, Ye; Pan, Chenghao; Shen, Zheyuan; Chen, Sikang; Xu, Lei; Dong, Xiaowu; Chen, Jing

Year: 2022

Venue: Evidence-based complementary and alternative medicine : eCAM

DOI: https://doi.org/10.1155/2022/4629392

Paper List of the compounds selected from propolis.

(14519913), Muhammad Bilal Azmi, (5628227), Simran Kumari, (21492547), Sakina Aquil, (21492550), Urooj Nizami, (21368142), Arisha Sohail, (14519922), Syed Danish Haseen Ahmed, (14157525), Shamim Akhtar Qureshi · 2025 · Figshare · DOI

Full title: List of the compounds selected from propolis.

Authors: (14519913), Muhammad Bilal Azmi, (5628227), Simran Kumari, (21492547), Sakina Aquil, (21492550), Urooj Nizami, (21368142), Arisha Sohail, (14519922), Syed Danish Haseen Ahmed, (14157525), Shamim Akhtar Qureshi

Year: 2025

Venue: Figshare

DOI: https://doi.org/10.1371/journal.pone.0324678.s002

Paper Learnt representations of proteins can be used for accurate prediction of small molecule binding sites on experimentally determined and predicted protein structures

Carbery, Anna; Buttenschoen, Martin; Skyner, R. et al. · 2024 · Journal of Cheminformatics · DOI

Full title: Learnt representations of proteins can be used for accurate prediction of small molecule binding sites on experimentally determined and predicted protein structures

Authors: Carbery, Anna; Buttenschoen, Martin; Skyner, R.; Delft, F. von; Deane, Charlotte M.

Year: 2024

Venue: Journal of Cheminformatics

DOI: https://doi.org/10.1186/s13321-024-00821-4

Paper KIFC1 inhibition: Exploring the potential of propolis-derived small molecules for targeting cancer progression through in silico analysis

Muhammad Bilal Azmi; Simran Kumari; Sakina Aquil et al. · 2025 · PLoS ONE · DOI

Full title: KIFC1 inhibition: Exploring the potential of propolis-derived small molecules for targeting cancer progression through in silico analysis

Authors: Muhammad Bilal Azmi; Simran Kumari; Sakina Aquil; Urooj Nizami; Arisha Sohail; Syed Danish Haseen Ahmed; S. Qureshi

Year: 2025

Venue: PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0324678

Paper Stepwise schematic workflow of the present study.

Full title: Stepwise schematic workflow of the present study.

Year: 2025

Venue: Figshare

DOI: https://doi.org/10.1371/journal.pone.0324678.g001

Paper An overview of recent advances and challenges in predicting compound-protein interaction (CPI)

Li, Yanbei; Fan, Zhehuan; Rao, Jingxin et al. · 2023 · Medical Review · DOI

Full title: An overview of recent advances and challenges in predicting compound-protein interaction (CPI)

Authors: Li, Yanbei; Fan, Zhehuan; Rao, Jingxin; Chen, Zhiyi; Chu, Qinyu; Zheng, Mingyue; Li, Xutong

Year: 2023

Venue: Medical Review

DOI: https://doi.org/10.1515/mr-2023-0030

Paper AI-Assisted chemical probe discovery for the understudied Calcium-Calmodulin Dependent Kinase, PNCK

Essegian, Derek J.; Chávez, Valery; Khurshid, Rabia et al. · 2023 · PLoS Computational Biology · DOI

Full title: AI-Assisted chemical probe discovery for the understudied Calcium-Calmodulin Dependent Kinase, PNCK

Authors: Essegian, Derek J.; Chávez, Valery; Khurshid, Rabia; Merchan, Jaime R.; Schürer, Stephan C.

Year: 2023

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1010263

Paper End-to-end sequence-structure-function meta-learning predicts genome-wide chemical-protein interactions for dark proteins

Cai, Tian; Xie, Li; Zhang, Shuo et al. · 2023 · PLoS Computational Biology · DOI

Full title: End-to-end sequence-structure-function meta-learning predicts genome-wide chemical-protein interactions for dark proteins

Authors: Cai, Tian; Xie, Li; Zhang, Shuo; Chen, Muge; He, Di; Badkul, Amitesh; Liu, Yang; Namballa, Hari Krishna; Dorogan, Michael; Harding, Wayne W.; Mura, Cameron; Bourne, Philip E.; Xie, Lei

Year: 2023

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1010851

Paper Modeling Protein-Ligand Interactions with Graph Convolutional Networks for Interpretable Pharmaceutical Discovery

Puentes, Paola Ruiz; Rueda-Gensini, Laura; Valderrama, Natalia et al. · 2022 · Research Square (Research Square) · DOI

Full title: Modeling Protein-Ligand Interactions with Graph Convolutional Networks for Interpretable Pharmaceutical Discovery

Authors: Puentes, Paola Ruiz; Rueda-Gensini, Laura; Valderrama, Natalia; Hernández, Isabela; González, Cristina; Daza, Laura; Muñoz-Camargo, Carolina; Cruz, Juan C.; Arbeláez, Pablo

Year: 2022

Venue: Research Square (Research Square)

DOI: https://doi.org/10.21203/rs.3.rs-1262123/v1

Paper Exploration of Dark Chemical Genomics Space viaPortal Learning: Applied to Targeting theUndruggable Genome and COVID-19 Anti-InfectivePolypharmacology

Cai, Tian; Xie, Li; Chen, Muge et al. · 2021 · Research Square (Research Square) · DOI

Full title: Exploration of Dark Chemical Genomics Space viaPortal Learning: Applied to Targeting theUndruggable Genome and COVID-19 Anti-InfectivePolypharmacology

Authors: Cai, Tian; Xie, Li; Chen, Muge; Liu, Yang; He, Di; Zhang, Shuo; Mura, Cameron; Bourne, Philip E.; Xie, Lei

Year: 2021

Venue: Research Square (Research Square)

DOI: https://doi.org/10.21203/rs.3.rs-1109318/v1

Paper Accurate Protein-Ligand Complex Structure Prediction using Geometric Deep Learning

Zhang, Junfeng; He, Kelei; Dong, Tiejun et al. · 2022 · DOI

Full title: Accurate Protein-Ligand Complex Structure Prediction using Geometric Deep Learning

Authors: Zhang, Junfeng; He, Kelei; Dong, Tiejun; Wu, Jinhui

Year: 2022

DOI: https://doi.org/10.21203/rs.3.rs-1454132/v1

Paper One substrate many enzymes virtual screening uncovers missing genes of carnitine biosynthesis in human and mouse.

Malatesta, Marco; Fornasier, Emanuele; Di Salvo, Martino Luigi et al. · 2024 · Nature communications · DOI

Full title: One substrate many enzymes virtual screening uncovers missing genes of carnitine biosynthesis in human and mouse.

Year: 2024

Venue: Nature communications

DOI: https://doi.org/10.1038/s41467-024-47466-3

Paper Lira: Rotational Invariant Shape and Electrostatic Descriptors for Small Molecules based on Real Spherical Harmonics

Montalvão, Rinaldo W., Caires, Fernando R., Silva, Samuel, Veríssimo-Alves, Marcos, Pinheiro, Vitor B. · 2023 · Research Square (Research Square) · DOI

Full title: Lira: Rotational Invariant Shape and Electrostatic Descriptors for Small Molecules based on Real Spherical Harmonics

Authors: Montalvão, Rinaldo W., Caires, Fernando R., Silva, Samuel, Veríssimo-Alves, Marcos, Pinheiro, Vitor B.

Year: 2023

Venue: Research Square (Research Square)

DOI: https://doi.org/10.21203/rs.3.rs-3153941/v1

Paper 3DinforCPI: Enhancing Efficiency of Compound-Protein Interaction Prediction Through Novel Perspectives on Multi-level Information Integration

Nguyen, Ngoc-Quang; Park, Sejeong; Gim, Mogan et al. · 2023 · Research Square (Research Square) · DOI

Full title: 3DinforCPI: Enhancing Efficiency of Compound-Protein Interaction Prediction Through Novel Perspectives on Multi-level Information Integration

Authors: Nguyen, Ngoc-Quang; Park, Sejeong; Gim, Mogan; Kang, Jaewoo

Year: 2023

Venue: Research Square (Research Square)

DOI: https://doi.org/10.21203/rs.3.rs-3305654/v1

Paper DynamicBind: predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model

Lu, Wei; Zhang, Jixian; Huang, Weifeng et al. · 2024 · Nature Communications · DOI

Full title: DynamicBind: predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model

Authors: Lu, Wei; Zhang, Jixian; Huang, Weifeng; Zhang, Ziqiao; Jia, Xiangyu; Wang, Zhenyu; Shi, Leilei; Li, Chengtao; Wolynes, Peter G.; Zheng, Shuangjia

Year: 2024

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-024-45461-2

Paper Inferring molecular inhibition potency with AlphaFold predicted structures

Oliveira, Pedro F.; Guedes, Rita C.; Falcão, André O. · 2024 · Scientific Reports · DOI

Full title: Inferring molecular inhibition potency with AlphaFold predicted structures

Authors: Oliveira, Pedro F.; Guedes, Rita C.; Falcão, André O.

Year: 2024

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-024-58394-z

Paper Structure prediction of protein-ligand complexes from sequence information with Umol

Bryant, Patrick; Kelkar, Atharva; Guljas, Andrea et al. · 2023 · DOI

Full title: Structure prediction of protein-ligand complexes from sequence information with Umol

Authors: Bryant, Patrick; Kelkar, Atharva; Guljas, Andrea; Clementi, Cecilia; Noé, Frank

Year: 2023

DOI: https://doi.org/10.1101/2023.11.03.565471

Paper Sequence-based drug design using transformers

Zhang, Shengyu; Huo, Donghui; Horne, Robert I. et al. · 2023 · Research Square (Research Square) · DOI

Full title: Sequence-based drug design using transformers

Authors: Zhang, Shengyu; Huo, Donghui; Horne, Robert I.; Qi, Yumeng; Ojeda, Sebastian Pujalte; Yan, Aixia; Vendruscolo, Michele

Year: 2023

Venue: Research Square (Research Square)

DOI: https://doi.org/10.1101/2023.11.27.568880

Paper PackDock: a Diffusion Based Side Chain Packing Model for Flexible Protein-Ligand Docking

Zhang, Runze; Jiang, Xinyu; Cao, Duanhua et al. · 2024 · DOI

Full title: PackDock: a Diffusion Based Side Chain Packing Model for Flexible Protein-Ligand Docking

Authors: Zhang, Runze; Jiang, Xinyu; Cao, Duanhua; Yu, Jie; Chen, Mingan; Fan, Zhehuan; Kong, Xiangtai; Xiong, Jiacheng; Zhang, Zimei; Zhang, Wei; Ni, Shengkun; Wang, Yitian; Gao, Shenghua; Zheng, Mingyue

Year: 2024

DOI: https://doi.org/10.1101/2024.01.31.578200

Paper Revolutionizing Healthcare: AI-driven Innovations in Drug Development and Personalized Medicine

Jaitawat, Dhruv Pratap SIngh, Chauhan, Shikha Baghel, Jain, Chirag, Singh, Indu · 2025 · Current pharmacogenomics and personalized medicine (Online)/Current pharmacogenomics and personalized medicine · DOI

Full title: Revolutionizing Healthcare: AI-driven Innovations in Drug Development and Personalized Medicine

Authors: Jaitawat, Dhruv Pratap SIngh, Chauhan, Shikha Baghel, Jain, Chirag, Singh, Indu

Year: 2025

Venue: Current pharmacogenomics and personalized medicine (Online)/Current pharmacogenomics and personalized medicine

DOI: https://doi.org/10.2174/0118756921395626250905121219

Paper Computational Approaches to Molecular Docking and Protein Modeling in Drug Discovery

Jagtap, Monali; Girnar, Ghanshyam; Ahuja, Vijay T. · 2025 · Journal of Drug Delivery and Therapeutics · DOI

Full title: Computational Approaches to Molecular Docking and Protein Modeling in Drug Discovery

Authors: Jagtap, Monali; Girnar, Ghanshyam; Ahuja, Vijay T.

Year: 2025

Venue: Journal of Drug Delivery and Therapeutics

DOI: https://doi.org/10.22270/jddt.v15i6.7212

Paper Conformational changes in the AdeB transmembrane efflux pump by amphiphilic peptide Mastoparan-B, down-regulates expression of the ade B Gene and restores antibiotics Susceptibility

Shakibaie, Mohammad Reza; Modaresi, Farzan; Azizi, Omid et al. · 2023 · DOI

Full title: Conformational changes in the AdeB transmembrane efflux pump by amphiphilic peptide Mastoparan-B, down-regulates expression of the ade B Gene and restores antibiotics Susceptibility

Authors: Shakibaie, Mohammad Reza; Modaresi, Farzan; Azizi, Omid; Tadjrobehkar, Omid; Ghaemi, Mohammad Mehdi

Year: 2023

DOI: https://doi.org/10.1101/2023.01.03.522678

Paper Evaluation of AlphaFold-derived Structures for Earlystage Virtual Screening: Utility and Limitations

Atsumi, Kota · 2026 · DOI

Full title: Evaluation of AlphaFold-derived Structures for Earlystage Virtual Screening: Utility and Limitations

Authors: Atsumi, Kota

Year: 2026

DOI: https://doi.org/10.26434/chemrxiv.15000478/v1

Paper Comparative structural insights and functional analysis for the distinct unbound states of Human AGO proteins

Kakoulidis, Panos; Theotoki, Eleni I.; Pantazopoulou, Vasiliki I. et al. · 2024 · Research Square (Research Square) · DOI

Full title: Comparative structural insights and functional analysis for the distinct unbound states of Human AGO proteins

Authors: Kakoulidis, Panos; Theotoki, Eleni I.; Pantazopoulou, Vasiliki I.; Vlachos, Ioannis S.; Emiris, Ioannis Z.; Stravopodis, Dimitrios J.; Anastasiadou, Ema

Year: 2024

Venue: Research Square (Research Square)

DOI: https://doi.org/10.21203/rs.3.rs-4058579/v1

Paper Poxviridae Protein kinases as targets for control of LSDV , Monkeypox like outbreaks

Amanchy, Ramars; Poornachandra, Yedla; Nalla, Saikumar et al. · 2023 · DOI

Full title: Poxviridae Protein kinases as targets for control of LSDV , Monkeypox like outbreaks

Authors: Amanchy, Ramars; Poornachandra, Yedla; Nalla, Saikumar; Racha, Vyshnavi; Bhamidipati, Pranav

Year: 2023

DOI: https://doi.org/10.22541/au.168865159.94168766/v1

Paper Automated benchmarking of combined protein structure and ligand conformation prediction

Robin, Xavier; Leemann, Michèle; Sagasta, Ander et al. · 2023 · DOI

Full title: Automated benchmarking of combined protein structure and ligand conformation prediction

Authors: Robin, Xavier; Leemann, Michèle; Sagasta, Ander; Eberhardt, Jérôme; Schwede, Torsten; Durairaj, Janani

Year: 2023

DOI: https://doi.org/10.22541/au.168382988.85108031/v1

Paper Cosolvent and Dynamic Effects in Binding Pocket Search by Docking Simulations

Szabó, P. Bernát; Zariquiey, Francesc Sabanés; Nogueira, Juan J. · 2021 · DOI

Full title: Cosolvent and Dynamic Effects in Binding Pocket Search by Docking Simulations

Authors: Szabó, P. Bernát; Zariquiey, Francesc Sabanés; Nogueira, Juan J.

Year: 2021

DOI: https://doi.org/10.26434/chemrxiv-2021-0dwfq

Paper DeepPocket: Ligand Binding Site Detection and Segmentation using 3D Convolutional Neural Networks

Aggarwal, Rishal, Gupta, Akash, Chelur, Vineeth, Jawahar, C. V., Priyakumar, U. Deva · 2021 · DOI

Full title: DeepPocket: Ligand Binding Site Detection and Segmentation using 3D Convolutional Neural Networks

Authors: Aggarwal, Rishal, Gupta, Akash, Chelur, Vineeth, Jawahar, C. V., Priyakumar, U. Deva

Year: 2021

DOI: https://doi.org/10.26434/chemrxiv.14611146.v1

Paper zPoseScore model for accurate and robust protein-ligand docking pose scoring in CASP15

Zheng, Liangzhen; Shen, Tao; Liu, Fuxu et al. · 2023 · DOI

Full title: zPoseScore model for accurate and robust protein-ligand docking pose scoring in CASP15

Authors: Zheng, Liangzhen; Shen, Tao; Liu, Fuxu; Wang, Zechen; Sun, Jinyuan; Bu, Yifan; Meng, Jintao; Chen, Weihua; Mu, Yuguang; Li, Weifeng; Zhao, Guoping; Wang, Sheng; Wei, Yanjie

Year: 2023

DOI: https://doi.org/10.22541/au.168170991.15467381/v1

Paper Uni-Mol: A Universal 3D Molecular Representation Learning Framework

Zhou, Gengmo; Gao, Zhifeng; Ding, Qiankun et al. · 2023 · DOI

Full title: Uni-Mol: A Universal 3D Molecular Representation Learning Framework

Authors: Zhou, Gengmo; Gao, Zhifeng; Ding, Qiankun; Zheng, Hang; Xu, Hongteng; Wei, Zhewei; Zhang, Linfeng; Ke, Guolin

Year: 2023

DOI: https://doi.org/10.26434/chemrxiv-2022-jjm0j-v4

Paper Benchmarking Refined and Unrefined AlphaFold2 Structures for Hit Discovery

Yuqi Zhang; Márton Vass; Da Shi et al. · 2023 · Journal of Chemical Information and Modeling · DOI

Full title: Benchmarking Refined and Unrefined AlphaFold2 Structures for Hit Discovery

Authors: Yuqi Zhang; Márton Vass; Da Shi; Esam T. Abualrous; J. Chambers; N. Chopra; C. Higgs; Koushik Kasavajhala; Hubert Li; P. Nandekar; Hideyuki Sato; E. B. Miller; Matthew P. Repasky; Steven V Jerome

Year: 2023

Venue: Journal of Chemical Information and Modeling

DOI: https://doi.org/10.1021/acs.jcim.2c01219

Paper Induced-Fit Docking Enables Accurate Free Energy Perturbation Calculations in Homology Models

Xu, Tianchuan; Zhu, Kai; Beautrait, Alexandre et al. · 2022 · DOI

Full title: Induced-Fit Docking Enables Accurate Free Energy Perturbation Calculations in Homology Models

Authors: Xu, Tianchuan; Zhu, Kai; Beautrait, Alexandre; Vendôme, Jérémie; Borrelli, Kenneth; Abel, Robert; Friesner, Richard A.; Miller, Edward B.

Year: 2022

DOI: https://doi.org/10.26434/chemrxiv-2022-mq9n3

Paper Addressing sub-optimal poses in non-equilibrium alchemical calculations

Karrenbrock, Maurice; Rizzi, Valerio; Procacci, Piero et al. · 2023 · DOI

Full title: Addressing sub-optimal poses in non-equilibrium alchemical calculations

Authors: Karrenbrock, Maurice; Rizzi, Valerio; Procacci, Piero; Gervasio, Francesco Luigi

Year: 2023

DOI: https://doi.org/10.26434/chemrxiv-2023-29682

Paper How good are AlphaFold models for docking-based virtual screening?

Scardino, Valeria; Filippo, Juan I. Di; Cavasotto, Claudio N. · 2022 · DOI

Full title: How good are AlphaFold models for docking-based virtual screening?

Authors: Scardino, Valeria; Filippo, Juan I. Di; Cavasotto, Claudio N.

Year: 2022

DOI: https://doi.org/10.26434/chemrxiv-2022-sgj8c

Paper Benchmarking Refined and Unrefined AlphaFold2 Structures for Hit Discovery

Yuqi Zhang; Márton Vass; Da Shi et al. · 2023 · Journal of Chemical Information and Modeling · DOI

Full title: Benchmarking Refined and Unrefined AlphaFold2 Structures for Hit Discovery

Year: 2023

Venue: Journal of Chemical Information and Modeling

DOI: https://doi.org/10.1021/acs.jcim.2c01219

Paper Using AlphaFold and Experimental Structures for the Prediction of the Structure and Binding Affinities of GPCR Complexes via In-duced Fit Docking and Free Energy Perturbation

Coskun, Dilek; Lihan, Muyun; Rodrigues, João et al. · 2023 · DOI

Full title: Using AlphaFold and Experimental Structures for the Prediction of the Structure and Binding Affinities of GPCR Complexes via In-duced Fit Docking and Free Energy Perturbation

Authors: Coskun, Dilek; Lihan, Muyun; Rodrigues, João; Vass, Marton; Robinson, Daniel P.; Friesner, Richard A.; Miller, Edward B.

Year: 2023

DOI: https://doi.org/10.26434/chemrxiv-2023-hsvx6-v3

Paper Augmentation of Structure Information to the Sequence-Based Machine Learning-Assisted Directed Protein Evolution

Yutzy, Lane D., Nguyen, Kenny, Vallet, Peter, Yu, Jielin, He, Ronggui, Li, Jianxiong, Yan, Le, Kim, Joohyun, Jung, Jangwook P. · 2023 · DOI

Full title: Augmentation of Structure Information to the Sequence-Based Machine Learning-Assisted Directed Protein Evolution

Authors: Yutzy, Lane D., Nguyen, Kenny, Vallet, Peter, Yu, Jielin, He, Ronggui, Li, Jianxiong, Yan, Le, Kim, Joohyun, Jung, Jangwook P.

Year: 2023

DOI: https://doi.org/10.26434/chemrxiv-2023-llpnk

Paper Comparative Structure-Based Virtual Screening Utilizing Optimized AlphaFold Model Identifies Selective HDAC11 Inhibitor.

Baselious, Fady; Hilscher, Sebastian; Robaa, Dina et al. · 2024 · International journal of molecular sciences · DOI

Full title: Comparative Structure-Based Virtual Screening Utilizing Optimized AlphaFold Model Identifies Selective HDAC11 Inhibitor.

Authors: Baselious, Fady; Hilscher, Sebastian; Robaa, Dina; Barinka, Cyril; Schutkowski, Mike; Sippl, Wolfgang

Year: 2024

Venue: International journal of molecular sciences

DOI: https://doi.org/10.3390/ijms25021358

Paper DSDPFlex: An Improved Flexible-Receptor Docking Method with GPU Acceleration

Dong, Chengwei; Huang, Yupeng; Lin, Xiaohan et al. · 2023 · DOI

Full title: DSDPFlex: An Improved Flexible-Receptor Docking Method with GPU Acceleration

Authors: Dong, Chengwei; Huang, Yupeng; Lin, Xiaohan; Zhang, Hong; Gao, Yi Qin

Year: 2023

DOI: https://doi.org/10.26434/chemrxiv-2023-bcw0g-v2

Paper Comparative Structure-Based Virtual Screening Utilizing Optimized AlphaFold Model Identifies Selective HDAC11 Inhibitor.

Baselious, Fady; Hilscher, Sebastian; Robaa, Dina et al. · 2024 · International journal of molecular sciences · DOI

Full title: Comparative Structure-Based Virtual Screening Utilizing Optimized AlphaFold Model Identifies Selective HDAC11 Inhibitor.

Authors: Baselious, Fady; Hilscher, Sebastian; Robaa, Dina; Barinka, Cyril; Schutkowski, Mike; Sippl, Wolfgang

Year: 2024

Venue: International journal of molecular sciences

DOI: https://doi.org/10.3390/ijms25021358

Paper Augmentation of Structure Information to the Sequence-Based Machine Learning-Assisted Directed Protein Evolution

Yutzy, Lane D.; Nguyen, Kenny; Vallet, Peter et al. · 2024 · DOI

Full title: Augmentation of Structure Information to the Sequence-Based Machine Learning-Assisted Directed Protein Evolution

Authors: Yutzy, Lane D.; Nguyen, Kenny; Vallet, Peter; Li, Jianxiong; Yu, Jielin; He, Ronggui; Yan, Le; Kim, Joohyun; Jung, Jangwook P.

Year: 2024

DOI: https://doi.org/10.26434/chemrxiv-2023-llpnk-v3

Paper DSDPFlex: An Improved Flexible-Receptor Docking Method with GPU Acceleration

Dong, Chengwei; Huang, Yupeng; Lin, Xiaohan et al. · 2023 · DOI

Full title: DSDPFlex: An Improved Flexible-Receptor Docking Method with GPU Acceleration

Authors: Dong, Chengwei; Huang, Yupeng; Lin, Xiaohan; Zhang, Hong; Gao, Yi Qin

Year: 2023

DOI: https://doi.org/10.26434/chemrxiv-2023-bcw0g-v2

Paper A Protein-Ligand Interaction-focused 3D Molecular Generative Framework for Generalizable Structure-based Drug Design

Zhung, Wonho; Kim, Hyeongwoo; Kim, Woo Youn · 2023 · DOI

Full title: A Protein-Ligand Interaction-focused 3D Molecular Generative Framework for Generalizable Structure-based Drug Design

Authors: Zhung, Wonho; Kim, Hyeongwoo; Kim, Woo Youn

Year: 2023

DOI: https://doi.org/10.26434/chemrxiv-2023-jsjwx

Paper Using AlphaFold and Experimental Structures for the Prediction of the Structure and Binding Affinities of GPCR Complexes via Induced Fit Docking and Free Energy Perturbation

Coskun, Dilek; Lihan, Muyun; Rodrigues, João et al. · 2023 · DOI

Full title: Using AlphaFold and Experimental Structures for the Prediction of the Structure and Binding Affinities of GPCR Complexes via Induced Fit Docking and Free Energy Perturbation

Authors: Coskun, Dilek; Lihan, Muyun; Rodrigues, João; Vass, Marton; Robinson, Daniel P.; Friesner, Richard A.; Miller, Edward B.

Year: 2023

DOI: https://doi.org/10.26434/chemrxiv-2023-hsvx6-v3

Paper A Computational Workflow for Refining AF2 Models in Drug Design Using Kinetic and Thermodynamic Binding Calculations: A Case Study for the Unresolved Inactive human Adenosine A3 Receptor

Kolocouris, Antonios; Stampelou, Margarita; Ladds, Graham · 2023 · DOI

Full title: A Computational Workflow for Refining AF2 Models in Drug Design Using Kinetic and Thermodynamic Binding Calculations: A Case Study for the Unresolved Inactive human Adenosine A3 Receptor

Authors: Kolocouris, Antonios; Stampelou, Margarita; Ladds, Graham

Year: 2023

DOI: https://doi.org/10.26434/chemrxiv-2023-llhdq

Paper Deep Learning Strategies for Enhanced Molecular Docking and Virtual Screening

Silva, Matheus Müller Pereira da; Guedes, Isabella Alvim; Custódio, Fábio Lima et al. · 2023 · DOI

Full title: Deep Learning Strategies for Enhanced Molecular Docking and Virtual Screening

Authors: Silva, Matheus Müller Pereira da; Guedes, Isabella Alvim; Custódio, Fábio Lima; Krempser, Eduardo; Dardenne, Laurent E.

Year: 2023

DOI: https://doi.org/10.26434/chemrxiv-2023-zfv87-v2

Paper Guided docking as a data generation approach facilitates structure-based machine learning on kinases

Backenköhler, Michael; Groß, Joschka; Wolf, Verena et al. · 2023 · DOI

Full title: Guided docking as a data generation approach facilitates structure-based machine learning on kinases

Authors: Backenköhler, Michael; Groß, Joschka; Wolf, Verena; Volkamer, Andrea

Year: 2023

DOI: https://doi.org/10.26434/chemrxiv-2023-prk53

Paper Using AlphaFold and Experimental Structures for the Prediction of the Structure and Binding Affinities of GPCR Complexes via Induced Fit Docking and Free Energy Perturbation

Coskun, Dilek; Lihan, Muyun; Rodrigues, João et al. · 2023 · DOI

Full title: Using AlphaFold and Experimental Structures for the Prediction of the Structure and Binding Affinities of GPCR Complexes via Induced Fit Docking and Free Energy Perturbation

Authors: Coskun, Dilek; Lihan, Muyun; Rodrigues, João; Vass, Marton; Robinson, Daniel P.; Friesner, Richard A.; Miller, Edward B.

Year: 2023

DOI: https://doi.org/10.26434/chemrxiv-2023-hsvx6-v3

Paper Augmentation of Structure Information to the Sequence-Based Machine Learning-Assisted Directed Protein Evolution

Yutzy, Lane D.; Nguyen, Kenny; Vallet, Peter et al. · 2024 · DOI

Full title: Augmentation of Structure Information to the Sequence-Based Machine Learning-Assisted Directed Protein Evolution

Authors: Yutzy, Lane D.; Nguyen, Kenny; Vallet, Peter; Li, Jianxiong; Yu, Jielin; He, Ronggui; Yan, Le; Kim, Joohyun; Jung, Jangwook P.

Year: 2024

DOI: https://doi.org/10.26434/chemrxiv-2023-llpnk-v3

Paper Utilization of AlphaFold Models for Drug Discovery: Feasibility and Challenges. Histone Deacetylase 11 as a Case Study

Baselious, Fady; Robaa, Dina; Sippl, Wolfgang · 2023 · DOI

Full title: Utilization of AlphaFold Models for Drug Discovery: Feasibility and Challenges. Histone Deacetylase 11 as a Case Study

Authors: Baselious, Fady; Robaa, Dina; Sippl, Wolfgang

Year: 2023

DOI: https://doi.org/10.26434/chemrxiv-2023-rtjcx

Paper ACFIS 2.0: an improved web-server for fragment-based drug discovery via a dynamic screening strategy

Shi, Xing-Xing; Wang, Zhi-Zheng; Wang, Fan et al. · 2023 · Nucleic Acids Research · DOI

Full title: ACFIS 2.0: an improved web-server for fragment-based drug discovery via a dynamic screening strategy

Authors: Shi, Xing-Xing; Wang, Zhi-Zheng; Wang, Fan; Hao, Ge‐Fei; Yang, Guang‐Fu

Year: 2023

Venue: Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gkad348

Paper SH2db, an information system for the SH2 domain

Bajusz, Dávid; Pándy‐Szekeres, Gáspár; Takács, Ágnes et al. · 2023 · Nucleic Acids Research · DOI

Full title: SH2db, an information system for the SH2 domain

Authors: Bajusz, Dávid; Pándy‐Szekeres, Gáspár; Takács, Ágnes; Araujo, Elvin D. de; Keserű, György M.

Year: 2023

Venue: Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gkad420

Paper BioLiP2: an updated structure database for biologically relevant ligand–protein interactions

Zhang, Chengxin, Zhang, Xi, Freddolino, Peter L., Zhang, Yang · 2023 · Nucleic Acids Research · DOI

Full title: BioLiP2: an updated structure database for biologically relevant ligand–protein interactions

Authors: Zhang, Chengxin, Zhang, Xi, Freddolino, Peter L., Zhang, Yang

Year: 2023

Venue: Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gkad630

Paper SARS-CoV-2 3D database: understanding the coronavirus proteome and evaluating possible drug targets

Alsulami, Ali F.; Thomas, S.E.; Jamasb, Arian R. et al. · 2020 · Briefings in Bioinformatics · DOI

Full title: SARS-CoV-2 3D database: understanding the coronavirus proteome and evaluating possible drug targets

Authors: Alsulami, Ali F.; Thomas, S.E.; Jamasb, Arian R.; Beaudoin, Christopher A.; Moghul, Ismail; Bannerman, Bridget P.; Copoiu, Liviu; Vedithi, Sundeep Chaitanya; Torres, Pedro Henrique Monteiro; Blundell, Tom L.

Year: 2020

Venue: Briefings in Bioinformatics

DOI: https://doi.org/10.1093/bib/bbaa404

Paper Proteins Plus : a comprehensive collection of web-based molecular modeling tools

Stierand, Katrin; Diedrich, Konrad; Ehrt, Christiane et al. · 2022 · Nucleic Acids Research · DOI

Full title: Proteins Plus : a comprehensive collection of web-based molecular modeling tools

Authors: Stierand, Katrin; Diedrich, Konrad; Ehrt, Christiane; Flachsenberg, Florian; Graef, Joel; Sieg, Jochen; Penner, Patrick; Poppinga, Martin; Ungethüm, Annett; Rarey, Matthias

Year: 2022

Venue: Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gkac305

Paper Extracellular loop 2 of G protein-coupled olfactory receptors is critical for odorant recognition

Yu, Yiqun; Pacalon, Jody; Ma, Zhenjie et al. · 2021 · DOI

Full title: Extracellular loop 2 of G protein-coupled olfactory receptors is critical for odorant recognition

Authors: Yu, Yiqun; Pacalon, Jody; Ma, Zhenjie; Xu, Lun; Belloir, Christine; Topin, Jérémie; Briand, Loı̈c; Golebiowski, Jérôme; Cong, Xiaojing

Year: 2021

DOI: https://doi.org/10.1101/2021.10.26.465980

Paper Generative AI in drug discovery and development: the next revolution of drug discovery and development would be directed by generative AI

Chakraborty, Chiranjib, Bhattacharya, Manojit, Pal, Soumen, Islam, Md. Aminul · 2024 · Annals of Medicine and Surgery · DOI

Full title: Generative AI in drug discovery and development: the next revolution of drug discovery and development would be directed by generative AI

Authors: Chakraborty, Chiranjib, Bhattacharya, Manojit, Pal, Soumen, Islam, Md. Aminul

Year: 2024

Venue: Annals of Medicine and Surgery

DOI: https://doi.org/10.1097/ms9.0000000000002438

Paper Transferability of Geometric Patterns from Protein Self-Interactions to Protein-Ligand Interactions

Koehl, Antoine; Jagota, Milind; Erdmann-Pham, Dan D. et al. · 2021 · DOI

Full title: Transferability of Geometric Patterns from Protein Self-Interactions to Protein-Ligand Interactions

Authors: Koehl, Antoine; Jagota, Milind; Erdmann-Pham, Dan D.; Fung, Alexander; Song, Yun S.

Year: 2021

DOI: https://doi.org/10.1101/2021.10.01.462692

Paper AlphaDrug: protein target specific de novo molecular generation

Qian, Hao; Lin, Cheng; Zhao, Dengwei et al. · 2022 · PNAS Nexus · DOI

Full title: AlphaDrug: protein target specific de novo molecular generation

Authors: Qian, Hao; Lin, Cheng; Zhao, Dengwei; Tu, Shikui; Xu, Lei

Year: 2022

Venue: PNAS Nexus

DOI: https://doi.org/10.1093/pnasnexus/pgac227

Paper Assessing Protein Homology Models with Docking Reproducibility

Plonski, Alexander P.; Reed, Scott M. · 2022 · DOI

Full title: Assessing Protein Homology Models with Docking Reproducibility

Authors: Plonski, Alexander P.; Reed, Scott M.

Year: 2022

DOI: https://doi.org/10.1101/2022.02.17.480964

Paper Enhanced compound-protein binding affinity prediction by representing protein multimodal information via a coevolutionary strategy

Guo, Binjie; Zheng, Hanyu; Jiang, Haohan et al. · 2022 · DOI

Full title: Enhanced compound-protein binding affinity prediction by representing protein multimodal information via a coevolutionary strategy

Authors: Guo, Binjie; Zheng, Hanyu; Jiang, Haohan; Li, Xiaodan; Guan, Naiyu; Zuo, Yanming; Zhang, Yicheng; Yang, Hengfu; Wang, Xuhua

Year: 2022

DOI: https://doi.org/10.1101/2022.04.06.487274

Paper AlphaFold Models Illuminate Half of Dark Human Proteins

Jessica L. Binder; J. Berendzen; Amy O. Stevens et al. · 2021 · bioRxiv · DOI

Full title: AlphaFold Models Illuminate Half of Dark Human Proteins

Authors: Jessica L. Binder; J. Berendzen; Amy O. Stevens; Yi He; Jian Wang; N. Dokholyan; Tudor I. Oprea

Year: 2021

Venue: bioRxiv

DOI: https://doi.org/10.1101/2021.11.04.467322

Paper Ligand Binding Prediction using Protein Structure Graphs and Residual Graph Attention Networks

Pandey, Mohit; Radaeva, Mariia; Mslati, Hazem et al. · 2022 · DOI

Full title: Ligand Binding Prediction using Protein Structure Graphs and Residual Graph Attention Networks

Authors: Pandey, Mohit; Radaeva, Mariia; Mslati, Hazem; Garland, Olivia; Fernández, Michael; Ester, Martin; Cherkasov, Artem

Year: 2022

DOI: https://doi.org/10.1101/2022.04.27.489750

Paper Computational model of the full-length TSH receptor

Mezei, Mihaly; Latif, Rauf; Davies, Terry F. · 2022 · DOI

Full title: Computational model of the full-length TSH receptor

Authors: Mezei, Mihaly; Latif, Rauf; Davies, Terry F.

Year: 2022

DOI: https://doi.org/10.1101/2022.07.13.499955

Paper AI-Assisted chemical probe discovery for the understudied Calcium-Calmodulin Dependent Kinase, PNCK

Essegian, Derek J.; Chávez, Valery; Khurshid, Rabia et al. · 2023 · PLoS Computational Biology · DOI

Full title: AI-Assisted chemical probe discovery for the understudied Calcium-Calmodulin Dependent Kinase, PNCK

Authors: Essegian, Derek J.; Chávez, Valery; Khurshid, Rabia; Merchan, Jaime R.; Schürer, Stephan C.

Year: 2023

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1010263

Paper TANKBind: Trigonometry-Aware Neural NetworKs for Drug-Protein Binding Structure Prediction

Lu, Wei; Wu, Qifeng; Zhang, Jixian et al. · 2022 · DOI

Full title: TANKBind: Trigonometry-Aware Neural NetworKs for Drug-Protein Binding Structure Prediction

Authors: Lu, Wei; Wu, Qifeng; Zhang, Jixian; Rao, Jiahua; Li, Chengtao; Zheng, Shuangjia

Year: 2022

DOI: https://doi.org/10.1101/2022.06.06.495043

Paper PrePCI: A structure- and chemical similarity-informed database of predicted protein compound interactions

Trudeau, Stephen J.; Hwang, Howook; Mathur, Deepika et al. · 2022 · DOI

Full title: PrePCI: A structure- and chemical similarity-informed database of predicted protein compound interactions

Authors: Trudeau, Stephen J.; Hwang, Howook; Mathur, Deepika; Begum, Kamrun; Petrey, Donald; Murray, Diana; Honig, Barry

Year: 2022

DOI: https://doi.org/10.1101/2022.09.17.508184

Paper Binding Site-enhanced Sequence Pretraining and Out-of-cluster Meta-learning Predict Genome-Wide Chemical-Protein Interactions for Dark Proteins

Cai, Tian; Xie, Li; Zhang, Shuo et al. · 2022 · DOI

Full title: Binding Site-enhanced Sequence Pretraining and Out-of-cluster Meta-learning Predict Genome-Wide Chemical-Protein Interactions for Dark Proteins

Authors: Cai, Tian; Xie, Li; Zhang, Shuo; Chen, Muge; He, Di; Badkul, Amitesh; Liu, Yang; Namballa, Hari Krishna; Dorogan, Michael; Harding, Wayne W.; Mura, Cameron; Bourne, Philip E.; Xie, Lei; Xie, Lei; Xie, Lei

Year: 2022

DOI: https://doi.org/10.1101/2022.11.15.516682

Paper Widely Used and Fast De Novo Drug Design by a Protein Sequence-Based Reinforcement Learning Model

Li, Yaqin; Li, Lingli; Xu, Yongjin et al. · 2022 · DOI

Full title: Widely Used and Fast De Novo Drug Design by a Protein Sequence-Based Reinforcement Learning Model

Authors: Li, Yaqin; Li, Lingli; Xu, Yongjin; Yu, Yi

Year: 2022

DOI: https://doi.org/10.1101/2022.08.18.504370

Paper Are Deep Learning Structural Models Sufficiently Accurate for Virtual Screening? Application of Docking Algorithms to AlphaFold2 Predicted Structures

Díaz-Rovira, Anna M.; Martín, Helena; Beuming, Thijs et al. · 2022 · DOI

Full title: Are Deep Learning Structural Models Sufficiently Accurate for Virtual Screening? Application of Docking Algorithms to AlphaFold2 Predicted Structures

Authors: Díaz-Rovira, Anna M.; Martín, Helena; Beuming, Thijs; Díaz, Lucía; Guallar, Vı́ctor; Ray, Soumya S.

Year: 2022

DOI: https://doi.org/10.1101/2022.08.18.504412

Paper Inhibiting a promiscuous GPCR: iterative discovery of bitter taste receptor ligands

Fierro, Fabrizio; Peri, Lior; Hübner, Harald et al. · 2022 · DOI

Full title: Inhibiting a promiscuous GPCR: iterative discovery of bitter taste receptor ligands

Authors: Fierro, Fabrizio; Peri, Lior; Hübner, Harald; Tabor-Schkade, Alina; Waterloo, Lukas; Löber, Stefan; Pfeiffer, Tara; Weikert, Dorothée; Dingjan, Tamir; Margulis, Eitan; Gmeiner, Peter; Niv, Masha Y.

Year: 2022

DOI: https://doi.org/10.1101/2022.11.24.517821

Paper BindingSiteAugmentedDTA: Enabling A Next-Generation Pipeline for Interpretable Prediction Models in Drug-Repurposing

Yousefi, Niloofar; Yazdani-Jahromi, Mehdi; Tayebi, Aida et al. · 2022 · DOI

Full title: BindingSiteAugmentedDTA: Enabling A Next-Generation Pipeline for Interpretable Prediction Models in Drug-Repurposing

Authors: Yousefi, Niloofar; Yazdani-Jahromi, Mehdi; Tayebi, Aida; Kolanthai, Elayaraja; Neal, Craig J.; Banerjee, Tanumoy; Gosai, Agnivo; Balasubramanian, Ganesh; Seal, Sudipta; Garibay, Özlem Özmen

Year: 2022

DOI: https://doi.org/10.1101/2022.08.30.505897

Paper PIsToN: Evaluating Protein Binding Interfaces with Transformer Networks

Stebliankin, Vitalii; Shirali, Azam; Baral, Prabin et al. · 2023 · DOI

Full title: PIsToN: Evaluating Protein Binding Interfaces with Transformer Networks

Authors: Stebliankin, Vitalii; Shirali, Azam; Baral, Prabin; Chapagain, Prem P.; Narasimhan, Giri

Year: 2023

DOI: https://doi.org/10.1101/2023.01.03.522623

Paper The structure, catalytic mechanism, and inhibitor identification of phosphatidylinositol remodeling MBOAT7

Wang, Kun; Lee, Chia‐Wei; Sui, Xuewu et al. · 2022 · DOI

Full title: The structure, catalytic mechanism, and inhibitor identification of phosphatidylinositol remodeling MBOAT7

Authors: Wang, Kun; Lee, Chia‐Wei; Sui, Xuewu; Kim, Siyoung; Wang, Shuhui; Higgs, Aidan; Baublis, Aaron J.; Voth, Gregory A.; Liao, Maofu; Walther, Tobias C.; Farese, Robert V.

Year: 2022

DOI: https://doi.org/10.1101/2022.09.15.508141

Paper Challenges in antibody structure prediction

Fernández‐Quintero, Monica L.; Kokot, Janik; Waibl, Franz et al. · 2022 · DOI

Full title: Challenges in antibody structure prediction

Authors: Fernández‐Quintero, Monica L.; Kokot, Janik; Waibl, Franz; Fischer, Anna-Lena M.; Quoika, Patrick K.; Deane, Charlotte M.; Liedl, Klaus R.

Year: 2022

DOI: https://doi.org/10.1101/2022.11.09.515600

Paper Investigating the conformational landscape of AlphaFold2-predicted protein kinase structures

Al-Masri, Carmen; Trozzi, Francesco; Lin, Shu-Hang et al. · 2023 · Bioinformatics Advances · DOI

Full title: Investigating the conformational landscape of AlphaFold2-predicted protein kinase structures

Authors: Al-Masri, Carmen; Trozzi, Francesco; Lin, Shu-Hang; Tran, Oanh; Sahni, Navriti; Pátek, Marcel; Cichońska, Anna; Ravikumar, Balaguru; Rahman, Rayees

Year: 2023

Venue: Bioinformatics Advances

DOI: https://doi.org/10.1093/bioadv/vbad129

Paper End-to-end protein–ligand complex structure generation with diffusion-based generative models

Nakata, Shuya; Mori, Y.; Tanaka, Shigenori · 2023 · BMC Bioinformatics · DOI

Full title: End-to-end protein–ligand complex structure generation with diffusion-based generative models

Authors: Nakata, Shuya; Mori, Y.; Tanaka, Shigenori

Year: 2023

Venue: BMC Bioinformatics

DOI: https://doi.org/10.1186/s12859-023-05354-5

Paper ImmuneBuilder: Deep-Learning models for predicting the structures of immune proteins

Abanades, Brennan; Wong, Wing Ki; Boyles, Fergus et al. · 2023 · Communications Biology · DOI

Full title: ImmuneBuilder: Deep-Learning models for predicting the structures of immune proteins

Authors: Abanades, Brennan; Wong, Wing Ki; Boyles, Fergus; Georges, Guy; Bujotzek, Alexander; Deane, Charlotte M.

Year: 2023

Venue: Communications Biology

DOI: https://doi.org/10.1038/s42003-023-04927-7

Paper Discovery of a cryptic pocket in the AI-predicted structure of PPM1D phosphatase explains the binding site and potency of its allosteric inhibitors.

Meller, Artur; De Oliveira, Saulo; Davtyan, Aram et al. · 2023 · Frontiers in molecular biosciences · DOI

Full title: Discovery of a cryptic pocket in the AI-predicted structure of PPM1D phosphatase explains the binding site and potency of its allosteric inhibitors.

Authors: Meller, Artur; De Oliveira, Saulo; Davtyan, Aram; Abramyan, Tigran; Bowman, Gregory R; van den Bedem, Henry

Year: 2023

Venue: Frontiers in molecular biosciences

DOI: https://doi.org/10.3389/fmolb.2023.1171143

Paper Structural insights into the heterotrimeric alternatively spliced P2X7 receptors

Salis, Sophie K. F. De; Chen, Zheng; Skarratt, Kristen K. et al. · 2023 · DOI

Full title: Structural insights into the heterotrimeric alternatively spliced P2X7 receptors

Authors: Salis, Sophie K. F. De; Chen, Zheng; Skarratt, Kristen K.; Fuller, Stephen J.; Balle, Thomas

Year: 2023

DOI: https://doi.org/10.1101/2023.05.30.542804

Paper Assessment of AlphaFold structures and optimization methods for virtual screening

Peng, Yanfei; Wu, Xia; Lin, Liang et al. · 2023 · DOI

Full title: Assessment of AlphaFold structures and optimization methods for virtual screening

Authors: Peng, Yanfei; Wu, Xia; Lin, Liang; Deng, Zhi-Luo; Zhao, Limin; Hao, Ke

Year: 2023

DOI: https://doi.org/10.1101/2023.01.10.523376

Paper Flexible protein–protein docking with a multitrack iterative transformer

Lee-Shin Chu; Jeffrey A. Ruffolo; Ameya Harmalkar et al. · 2023 · Protein Science · DOI

Full title: Flexible protein–protein docking with a multitrack iterative transformer

Authors: Lee-Shin Chu; Jeffrey A. Ruffolo; Ameya Harmalkar; Jeffrey J. Gray

Year: 2023

Venue: Protein Science

DOI: https://doi.org/10.1002/pro.4862

Paper PandoraRLO: DQN and Graph convolution based method for optimized ligand pose

Jose, Justin; Alam, Ujjaini; Singh, Divye et al. · 2023 · DOI

Full title: PandoraRLO: DQN and Graph convolution based method for optimized ligand pose

Authors: Jose, Justin; Alam, Ujjaini; Singh, Divye; Jatana, Nidhi; Arora, Pooja

Year: 2023

DOI: https://doi.org/10.1101/2023.03.12.532268

Paper Learnt representations of proteins can be used for accurate prediction of small molecule binding sites on experimentally determined and predicted protein structures

Carbery, Anna; Buttenschoen, Martin; Skyner, R. et al. · 2024 · Journal of Cheminformatics · DOI

Full title: Learnt representations of proteins can be used for accurate prediction of small molecule binding sites on experimentally determined and predicted protein structures

Authors: Carbery, Anna; Buttenschoen, Martin; Skyner, R.; Delft, F. von; Deane, Charlotte M.

Year: 2024

Venue: Journal of Cheminformatics

DOI: https://doi.org/10.1186/s13321-024-00821-4

Paper Exploring the Druggable Conformational Space of Protein Kinases Using AI-Generated Structures

Herrington, Noah B.; Stein, David; Li, Yan Chak et al. · 2023 · DOI

Full title: Exploring the Druggable Conformational Space of Protein Kinases Using AI-Generated Structures

Authors: Herrington, Noah B.; Stein, David; Li, Yan Chak; Pandey, Gaurav; Schlessinger, Avner

Year: 2023

DOI: https://doi.org/10.1101/2023.08.31.555779

Paper Design of Cyclic Peptides Targeting Protein–Protein Interactions Using AlphaFold

Kosugi, Takatsugu; Ohue, Masahito · 2023 · International Journal of Molecular Sciences · DOI

Full title: Design of Cyclic Peptides Targeting Protein–Protein Interactions Using AlphaFold

Authors: Kosugi, Takatsugu; Ohue, Masahito

Year: 2023

Venue: International Journal of Molecular Sciences

DOI: https://doi.org/10.3390/ijms241713257

Paper PSICHIC: physicochemical graph neural network for learning protein-ligand interaction fingerprints from sequence data

Koh, Huan Yee; Nguyen, Thi; Pan, Shirui et al. · 2023 · DOI

Full title: PSICHIC: physicochemical graph neural network for learning protein-ligand interaction fingerprints from sequence data

Authors: Koh, Huan Yee; Nguyen, Thi; Pan, Shirui; May, Lauren T.; Webb, Geoffrey I.

Year: 2023

DOI: https://doi.org/10.1101/2023.09.17.558145

Paper EquiScore: A generic protein-ligand interaction scoring method integrating physical prior knowledge with data augmentation modeling

Cao, Duanhua; Chen, Geng; Jiang, Jiaxin et al. · 2023 · DOI

Full title: EquiScore: A generic protein-ligand interaction scoring method integrating physical prior knowledge with data augmentation modeling

Authors: Cao, Duanhua; Chen, Geng; Jiang, Jiaxin; Yu, Jie; Zhang, Runze; Chen, Mingan; Zhang, Wei; Chen, Lifan; Zhong, Feisheng; Zhang, Yingying; Lu, Chenghao; Li, Xutong; Luo, Xiaomin; Zhang, Sulin; Zheng, Mingyue

Year: 2023

DOI: https://doi.org/10.1101/2023.06.18.545464

Paper Interpreting Molecular Dynamics Forces as Deep Learning Gradients Improves Quality Of Predicted Protein Structures

King, Jonathan; Koes, David Ryan · 2023 · DOI

Full title: Interpreting Molecular Dynamics Forces as Deep Learning Gradients Improves Quality Of Predicted Protein Structures

Authors: King, Jonathan; Koes, David Ryan

Year: 2023

DOI: https://doi.org/10.1101/2023.10.03.560775

Paper Generalized Biomolecular Modeling and Design with RoseTTAFold All-Atom

Krishna, Rohith; Wang, Jue; Ahern, Woody et al. · 2023 · DOI

Full title: Generalized Biomolecular Modeling and Design with RoseTTAFold All-Atom

Authors: Krishna, Rohith; Wang, Jue; Ahern, Woody; Sturmfels, Pascal; Venkatesh, Preetham; Kalvet, Indrek; Lee, Gyu Rie; Morey-Burrows, Felix S.; Anishchenko, Ivan; Humphreys, Ian R.; McHugh, R. Kathryn; Vafeados, Dionne; Li, Xinting; Sutherland, George A.; Hitchcock, Andrew; Hunter, C. Neil; Baek, Minkyung; DiMaio, Frank; Baker, David

Year: 2023

DOI: https://doi.org/10.1101/2023.10.09.561603

Paper Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with Attention

Smith, Zachary; Strobel, Michael; Vani, Bodhi P. et al. · 2023 · DOI

Full title: Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with Attention

Authors: Smith, Zachary; Strobel, Michael; Vani, Bodhi P.; Tiwary, Pratyush

Year: 2023

DOI: https://doi.org/10.1101/2023.07.25.550565

Paper GTExome: Modeling commonly expressed missense mutations in the human genome

Hoffman, Jill A.; Tan, Henry S.I.; Sandoval-Cooper, Clara et al. · 2023 · DOI

Full title: GTExome: Modeling commonly expressed missense mutations in the human genome

Authors: Hoffman, Jill A.; Tan, Henry S.I.; Sandoval-Cooper, Clara; Villiers, Kaelyn de; Reed, Scott M.

Year: 2023

DOI: https://doi.org/10.1101/2023.11.14.567143

Paper Structure prediction of protein-ligand complexes from sequence information with Umol

Bryant, Patrick; Kelkar, Atharva; Guljas, Andrea et al. · 2023 · DOI

Full title: Structure prediction of protein-ligand complexes from sequence information with Umol

Authors: Bryant, Patrick; Kelkar, Atharva; Guljas, Andrea; Clementi, Cecilia; Noé, Frank

Year: 2023

DOI: https://doi.org/10.1101/2023.11.03.565471

Paper AlphaFold2 structures template ligand discovery

Lyu, Jiankun; Kapolka, Nicholas J.; Gumpper, Ryan H. et al. · 2023 · DOI

Full title: AlphaFold2 structures template ligand discovery

Authors: Lyu, Jiankun; Kapolka, Nicholas J.; Gumpper, Ryan H.; Alon, Assaf; Wang, Liang; Jain, Manish K.; Barros-Álvarez, Ximena; Sakamoto, Kensuke; Kim, Yoojoong; DiBerto, Jeffrey F.; Kim, Kuglae; Tummino, Tia A.; Huang, Sijie; Irwin, John J.; Tarkhanova, Olga O.; Moroz, Yurii S.; Skiniotis, Georgios; Kruse, Andrew C.; Shoichet, Brian K.; Roth, Bryan L.

Year: 2023

DOI: https://doi.org/10.1101/2023.12.20.572662

Paper Towards the accurate modelling of antibody-antigen complexes from sequence using machine learning and information-driven docking

Giulini, Marco; Schneider, Constantin; Cutting, Daniel et al. · 2023 · DOI

Full title: Towards the accurate modelling of antibody-antigen complexes from sequence using machine learning and information-driven docking

Authors: Giulini, Marco; Schneider, Constantin; Cutting, Daniel; Desai, Nikita; Deane, Charlotte M.; Bonvin, Alexandre M. J. J.

Year: 2023

DOI: https://doi.org/10.1101/2023.11.17.567543

Paper Sequence-based drug design using transformers

Zhang, Shengyu; Huo, Donghui; Horne, Robert I. et al. · 2023 · DOI

Full title: Sequence-based drug design using transformers

Authors: Zhang, Shengyu; Huo, Donghui; Horne, Robert I.; Qi, Yumeng; Ojeda, Sebastian Pujalte; Yan, Aixia; Vendruscolo, Michele

Year: 2023

DOI: https://doi.org/10.1101/2023.11.27.568880

Paper A new paradigm for applying deep learning to protein–ligand interaction prediction

Wang, Zechen; Wang, Sheng; Li, Yangyang et al. · 2024 · Briefings in Bioinformatics · DOI

Full title: A new paradigm for applying deep learning to protein–ligand interaction prediction

Authors: Wang, Zechen; Wang, Sheng; Li, Yangyang; Guo, Jingjing; Wei, Yanjie; Mu, Yuguang; Zheng, Liangzhen; Li, Weifeng

Year: 2024

Venue: Briefings in Bioinformatics

DOI: https://doi.org/10.1093/bib/bbae145

Paper Benchmarking Reverse Docking through AlphaFold2 Human Proteome

Luo, Qing; Wang, Sheng; Li, HY et al. · 2023 · DOI

Full title: Benchmarking Reverse Docking through AlphaFold2 Human Proteome

Authors: Luo, Qing; Wang, Sheng; Li, HY; Zheng, Liangzhen; Mu, Yuguang; Guo, Jingjing

Year: 2023

DOI: https://doi.org/10.1101/2023.12.16.572027

Paper Molecular dynamics of outer membrane-embedded polysaccharide secretion porins reveals closed resting-state surface gates targetable by virtual fragment screening for drug hotspot identification

França, Tanos C. C.; Saïdi, Fares; Ajamian, Alain et al. · 2023 · DOI

Full title: Molecular dynamics of outer membrane-embedded polysaccharide secretion porins reveals closed resting-state surface gates targetable by virtual fragment screening for drug hotspot identification

Authors: França, Tanos C. C.; Saïdi, Fares; Ajamian, Alain; Islam, Salim T.; LaPlante, Steven R.

Year: 2023

DOI: https://doi.org/10.1101/2023.12.21.572922

Paper SurfDock is a Surface-Informed Diffusion Generative Model for Reliable and Accurate Protein-ligand Complex Prediction

Cao, Duanhua; Chen, Mingan; Zhang, Runze et al. · 2023 · DOI

Full title: SurfDock is a Surface-Informed Diffusion Generative Model for Reliable and Accurate Protein-ligand Complex Prediction

Authors: Cao, Duanhua; Chen, Mingan; Zhang, Runze; Yu, Jie; Jiang, Xinyu; Fan, Zhehuan; Zhang, Wei; Zheng, Mingyue

Year: 2023

DOI: https://doi.org/10.1101/2023.12.13.571408

Paper DrugHIVE: Target-specific spatial drug design and optimization with a hierarchical generative model

Weller, Jesse A.; Rohs, Remo · 2023 · DOI

Full title: DrugHIVE: Target-specific spatial drug design and optimization with a hierarchical generative model

Authors: Weller, Jesse A.; Rohs, Remo

Year: 2023

DOI: https://doi.org/10.1101/2023.12.22.573155

Paper PackDock: a Diffusion Based Side Chain Packing Model for Flexible Protein-Ligand Docking

Zhang, Runze; Jiang, Xinyu; Cao, Duanhua et al. · 2024 · DOI

Full title: PackDock: a Diffusion Based Side Chain Packing Model for Flexible Protein-Ligand Docking

Year: 2024

DOI: https://doi.org/10.1101/2024.01.31.578200

Paper SAXS DATA BASED GLYCOSYLATED MODELS OF HUMAN ALPHA-1-ACID GLYCORPROTEIN, A KEY PLAYER IN HEALTH, DISEASE AND DRUG CIRCULATION

Kalidas, Nidhi; Peddada, Nagesh; Pandey, Kalpana et al. · 2024 · DOI

Full title: SAXS DATA BASED GLYCOSYLATED MODELS OF HUMAN ALPHA-1-ACID GLYCORPROTEIN, A KEY PLAYER IN HEALTH, DISEASE AND DRUG CIRCULATION

Authors: Kalidas, Nidhi; Peddada, Nagesh; Pandey, Kalpana; Ashish, Fnu

Year: 2024

DOI: https://doi.org/10.1101/2024.02.01.578488

Paper Applying multi-state modeling using AlphaFold2 for kinases and its application for ensemble screening

Song, Jinung; Ha, Junsu; Lee, Juyong et al. · 2024 · DOI

Full title: Applying multi-state modeling using AlphaFold2 for kinases and its application for ensemble screening

Authors: Song, Jinung; Ha, Junsu; Lee, Juyong; Ko, Junsu; Shin, Woong‐Hee

Year: 2024

DOI: https://doi.org/10.1101/2024.04.04.588044

Paper PPIscreenML: Structure-based screening for protein-protein interactions using AlphaFold

Mischley, Victoria; Maier, Johannes; Chen, Jesse et al. · 2024 · DOI

Full title: PPIscreenML: Structure-based screening for protein-protein interactions using AlphaFold

Authors: Mischley, Victoria; Maier, Johannes; Chen, Jesse; Karanicolas, John

Year: 2024

DOI: https://doi.org/10.1101/2024.03.16.585347

Paper Comprehensive detection and characterization of human druggable pockets through novel binding site descriptors

Comajuncosa-Creus, Arnau; Jorba, Guillem; Barril, Xavier et al. · 2024 · DOI

Full title: Comprehensive detection and characterization of human druggable pockets through novel binding site descriptors

Authors: Comajuncosa-Creus, Arnau; Jorba, Guillem; Barril, Xavier; Aloy, Patrick

Year: 2024

DOI: https://doi.org/10.1101/2024.03.14.584971

Paper Protein language models are performant in structure-free virtual screening

Lam, Hilbert Yuen In; Guan, Jia Sheng; Ong, Xing Er et al. · 2024 · DOI

Full title: Protein language models are performant in structure-free virtual screening

Authors: Lam, Hilbert Yuen In; Guan, Jia Sheng; Ong, Xing Er; Pincket, Robbe; Mu, Yuguang

Year: 2024

DOI: https://doi.org/10.1101/2024.04.16.589765

Paper AlphaFold 3-enabled in silico exploration of PGAM1 interactions in cancer

Clarke, J.Jackson; Colcombe, James L.; Rigden, Daniel J. · 2025 · DOI

Full title: AlphaFold 3-enabled in silico exploration of PGAM1 interactions in cancer

Authors: Clarke, J.Jackson; Colcombe, James L.; Rigden, Daniel J.

Year: 2025

DOI: https://doi.org/10.1101/2025.06.23.661104

Paper Recent Developments in Ultralarge and Structure-Based Virtual Screening Approaches

Gorgulla, Christoph · 2023 · Annual Review of Biomedical Data Science · DOI

Full title: Recent Developments in Ultralarge and Structure-Based Virtual Screening Approaches

Authors: Gorgulla, Christoph

Year: 2023

Venue: Annual Review of Biomedical Data Science

DOI: https://doi.org/10.1146/annurev-biodatasci-020222-025013

Paper Tunable and Portable Extreme-Scale Drug Discovery Platform at Exascale

Palermo, Gianluca; Accordi, Gianmarco; Gadioli, Davide et al. · 2023 · DOI

Full title: Tunable and Portable Extreme-Scale Drug Discovery Platform at Exascale

Authors: Palermo, Gianluca; Accordi, Gianmarco; Gadioli, Davide; Vitali, Emanuele; Silvano, Cristina; Guindani, Bruno; Ardagna, Danilo; Beccari, Andrea R.; Bonanni, Domenico; Talarico, Carmine; Lughini, F.; Martinovič, Jan; Silva, Paulo; Böhm, Stanislav; Beránek, Jakub; Křenek, Jan; Jansı́k, Branislav; Cosenza, Biagio; Crisci, Luigi; Thoman, Peter; Salzmann, Philip; Fahringer, Thomas; Alexander, Leila T.; Tauriello, Gerardo; Schwede, Torsten; Durairaj, Janani; Emerson, Andrew; Ficarelli, Federico; Wingbermühle, Sebastian; Lindhal, E.; Gregori, Daniele; Sana, E.; Coletti, Silvano; Gschwandtner, Philipp

Year: 2023

DOI: https://doi.org/10.1145/3587135.3592172

Paper BioMolFormer: A Novel Approach to Molecular Generation with SELFIES and Monte Carlo Tree Search

Zhang, Yuntao; Liu, Lei; Liu, Y Q et al. · 2024 · DOI

Full title: BioMolFormer: A Novel Approach to Molecular Generation with SELFIES and Monte Carlo Tree Search

Authors: Zhang, Yuntao; Liu, Lei; Liu, Y Q; Wang, F.; Shi, Lijun

Year: 2024

DOI: https://doi.org/10.1145/3715931.3715941

Paper Evaluation of AlphaFold2 structures as docking targets

Holcomb, Matthew; Chang, Ya‐Ting; Goodsell, David S. et al. · 2022 · Protein Science · DOI

Full title: Evaluation of AlphaFold2 structures as docking targets

Authors: Holcomb, Matthew; Chang, Ya‐Ting; Goodsell, David S.; Forli, Stefano

Year: 2022

Venue: Protein Science

DOI: https://doi.org/10.1002/pro.4530

Paper The role of cholesterol binding in the control of cholesterol by the Scap–Insig system

Lee, Anthony G. · 2022 · European Biophysics Journal · DOI

Full title: The role of cholesterol binding in the control of cholesterol by the Scap–Insig system

Authors: Lee, Anthony G.

Year: 2022

Venue: European Biophysics Journal

DOI: https://doi.org/10.1007/s00249-022-01606-z

Paper zPoseScore model for accurate and robust protein–ligand docking pose scoring in CASP15

Shen, Tao; Liu, Fuxu; Wang, Zechen et al. · 2023 · Proteins Structure Function and Bioinformatics · DOI

Full title: zPoseScore model for accurate and robust protein–ligand docking pose scoring in CASP15

Authors: Shen, Tao; Liu, Fuxu; Wang, Zechen; Sun, Jinyuan; Bu, Yifan; Meng, Jintao; Chen, Weihua; Yao, Keyi; Mu, Yuguang; Li, Weifeng; Zhao, Guoping; Wang, Sheng; Wei, Yanjie; Zheng, Liangzhen

Year: 2023

Venue: Proteins Structure Function and Bioinformatics

DOI: https://doi.org/10.1002/prot.26573

Paper Protein‐Ligand Structure and Affinity Prediction in CASP16 Using a Geometric Deep Learning Ensemble and Flow Matching

Morehead, Alex; Liu, Jian; Neupane, Pawan et al. · 2025 · Proteins Structure Function and Bioinformatics · DOI

Full title: Protein‐Ligand Structure and Affinity Prediction in CASP16 Using a Geometric Deep Learning Ensemble and Flow Matching

Authors: Morehead, Alex; Liu, Jian; Neupane, Pawan; Giri, Nabin; Cheng, Jianlin

Year: 2025

Venue: Proteins Structure Function and Bioinformatics

DOI: https://doi.org/10.1002/prot.26827

Paper Toward physics‐based precision medicine: Exploiting protein dynamics to design new therapeutics and interpret variants

Meller, Artur; Kelly, Devin; Smith, Louis G. et al. · 2024 · Protein Science · DOI

Full title: Toward physics‐based precision medicine: Exploiting protein dynamics to design new therapeutics and interpret variants

Authors: Meller, Artur; Kelly, Devin; Smith, Louis G.; Bowman, Gregory R.

Year: 2024

Venue: Protein Science

DOI: https://doi.org/10.1002/pro.4902

Paper Keeping pace with the explosive growth of chemical libraries with structure‐based virtual screening

Kuan, Jacqueline; Radaeva, Mariia; Avenido, Adeline et al. · 2023 · Wiley Interdisciplinary Reviews Computational Molecular Science · DOI

Full title: Keeping pace with the explosive growth of chemical libraries with structure‐based virtual screening

Authors: Kuan, Jacqueline; Radaeva, Mariia; Avenido, Adeline; Cherkasov, Artem; Gentile, Francesco

Year: 2023

Venue: Wiley Interdisciplinary Reviews Computational Molecular Science

DOI: https://doi.org/10.1002/wcms.1678

Paper The effects of nature‐inspired amino acid substitutions on structural and biochemical properties of the E. coli L ‐asparaginase EcAIII

Janicki, Maciej; Ściuk, Anna; Zieleziński, Andrzej et al. · 2023 · Protein Science · DOI

Full title: The effects of nature‐inspired amino acid substitutions on structural and biochemical properties of the E. coli L ‐asparaginase EcAIII

Authors: Janicki, Maciej; Ściuk, Anna; Zieleziński, Andrzej; Ruszkowski, M.; Ludwików, Agnieszka; Karłowski, Wojciech M.; Jaskólski, Mariusz; Loch, Joanna I.

Year: 2023

Venue: Protein Science

DOI: https://doi.org/10.1002/pro.4647

Paper AlphaFold Kinase Optimizer: Enhancing Virtual Screening Performance Through Automated Refinement of AlphaFold-Based Kinase Structures.

Evteev, Sergei; Ivanenkov, Yan; Aiginin, Andrew et al. · 2026 · Proteins · DOI

Full title: AlphaFold Kinase Optimizer: Enhancing Virtual Screening Performance Through Automated Refinement of AlphaFold-Based Kinase Structures.

Authors: Evteev, Sergei; Ivanenkov, Yan; Aiginin, Andrew; Kuznetsov, Maksim; Shayakhmetov, Rim; Knyazev, Maksim; Bezrukov, Dmitry; Malyshev, Alex; Malkov, Maxim; Aliper, Alex; Zhavoronkov, Alex

Year: 2026

Venue: Proteins

DOI: https://doi.org/10.1002/prot.70056

Paper Drug repurposing for SARS-CoV-2: a high-throughput molecular docking, molecular dynamics, machine learning, and DFT study

Kashyap, Jatin; Datta, Dibakar · 2022 · Journal of Materials Science · DOI

Full title: Drug repurposing for SARS-CoV-2: a high-throughput molecular docking, molecular dynamics, machine learning, and DFT study

Authors: Kashyap, Jatin; Datta, Dibakar

Year: 2022

Venue: Journal of Materials Science

DOI: https://doi.org/10.1007/s10853-022-07195-8

Paper Evaluating GPCR modeling and docking strategies in the era of deep learning-based protein structure prediction.

Lee, Sumin; Kim, Seeun; Lee, Gyu Rie et al. · 2023 · Computational and structural biotechnology journal · DOI

Full title: Evaluating GPCR modeling and docking strategies in the era of deep learning-based protein structure prediction.

Authors: Lee, Sumin; Kim, Seeun; Lee, Gyu Rie; Kwon, Sohee; Woo, Hyeonuk; Seok, Chaok; Park, Hahnbeom

Year: 2023

Venue: Computational and structural biotechnology journal

DOI: https://doi.org/10.1016/j.csbj.2022.11.057

Paper Fungal Foe Unveiled: AlphaFold-based 3D structure prediction of Rhizopus delemar 1,3-β-Glucan synthase and virtual screening for the identification of potential inhibitors.

Kushwaha, Sandhya; Kumari, Deevena; Kumari, Sonia et al. · 2026 · In silico pharmacology · DOI

Full title: Fungal Foe Unveiled: AlphaFold-based 3D structure prediction of Rhizopus delemar 1,3-β-Glucan synthase and virtual screening for the identification of potential inhibitors.

Authors: Kushwaha, Sandhya; Kumari, Deevena; Kumari, Sonia; Sobhia, M Elizabeth

Year: 2026

Venue: In silico pharmacology

DOI: https://doi.org/10.1007/s40203-025-00546-8

Paper Beyond sequence: Structure-based machine learning

Durairaj, Janani; Ridder, Dick de; Dijk, Aalt D. J. van · 2022 · Computational and Structural Biotechnology Journal · DOI

Full title: Beyond sequence: Structure-based machine learning

Authors: Durairaj, Janani; Ridder, Dick de; Dijk, Aalt D. J. van

Year: 2022

Venue: Computational and Structural Biotechnology Journal

DOI: https://doi.org/10.1016/j.csbj.2022.12.039

Paper Identification of novel compounds against Trypanosoma cruzi using AlphaFold structures.

Ros-Lucas, Albert; Saeteros, Alejandra; Gabaldón-Figueira, Juan Carlos et al. · 2025 · Computational and structural biotechnology journal · DOI

Full title: Identification of novel compounds against Trypanosoma cruzi using AlphaFold structures.

Authors: Ros-Lucas, Albert; Saeteros, Alejandra; Gabaldón-Figueira, Juan Carlos; Martínez-Peinado, Nieves; Escabia, Elisa; Gascón, Joaquim; Alonso-Padilla, Julio

Year: 2025

Venue: Computational and structural biotechnology journal

DOI: https://doi.org/10.1016/j.csbj.2025.05.002

Paper AI protein structure prediction-based modeling and mutagenesis of a protostome receptor and peptide ligands reveal key residues for their interaction

Guo, Shi‐Qi; Li, Yadong; Chen, Ping et al. · 2022 · Journal of Biological Chemistry · DOI

Full title: AI protein structure prediction-based modeling and mutagenesis of a protostome receptor and peptide ligands reveal key residues for their interaction

Authors: Guo, Shi‐Qi; Li, Yadong; Chen, Ping; Zhang, Guo; Wang, Huiying; Jiang, Hui-Min; Liu, Weijia; Xu, Ju-Ping; Ding, Xueying; Fu, Ping; Yu, Ke; Zhou, Haibo; Checco, James W.; Jing, Jian

Year: 2022

Venue: Journal of Biological Chemistry

DOI: https://doi.org/10.1016/j.jbc.2022.102440

Paper Monomeric and dimeric states of human ZO1-PDZ2 are functional partners of the SARS-CoV-2 E protein

Giacon, Noah; Cascio, Ettore Lo; Davidson, Darcy S. et al. · 2023 · Computational and Structural Biotechnology Journal · DOI

Full title: Monomeric and dimeric states of human ZO1-PDZ2 are functional partners of the SARS-CoV-2 E protein

Authors: Giacon, Noah; Cascio, Ettore Lo; Davidson, Darcy S.; Polêto, Marcelo D.; Lemkul, Justin A.; Pennacchietti, Valeria; Pagano, Livia; Zamparelli, Carlotta; Toto, Angelo; Arcovito, Alessandro

Year: 2023

Venue: Computational and Structural Biotechnology Journal

DOI: https://doi.org/10.1016/j.csbj.2023.05.027

Paper Review: Applications of Machine Learning in Computer-Aided Drug Discovery — R0/PR3

Turzo, SM Bargeen Alam; Hantz, Eric R.; Lindert, Steffen et al. · 2022 · DOI

Full title: Review: Applications of Machine Learning in Computer-Aided Drug Discovery — R0/PR3

Authors: Turzo, SM Bargeen Alam; Hantz, Eric R.; Lindert, Steffen; Lindert, Steffen; Albawi, S; Mohammed, T; S, Al-Zawi; Alford, R; Leaver-Fay, A; Jeliazkov, J; Meara, O'; Dimaio, M; Park, F; Shapovalov, H; Renfrew, M; Mulligan, P; Kappel, V; Labonte, K; Pacella, J; Bonneau, M; Bradley, R; Dunbrack, P; Das, R; Baker, R; Kuhlman, D; Kortemme, B; Gray, T; J; Alhossary, A; Handoko, S; Mu, Y; Kwoh, C; Ali, A; Warsi, M; Rahman, M; Mj, Ahsan; Azam, F; Alon, A; Lyu, J; Braz, J; Tummino, T; Craik, V; Meara, O'; Webb, M; Radchenko, C; Moroz, D; Huang, Y; Liu, X-P; Roth, Y; Irwin, B; Basbaum, J; Shoichet, A; Kruse, B; A; Aprahamian, M; Tikunova, S; Price, M; Cuesta, A; Davis, J; Lindert, S; Ars-Pous, J; Patronov, A; Bjerrum, E; Tyrchan, C; Reymond, J; Engkvist, Chen; O; Baek, M; Dimaio, F; Anishchenko, I; Dauparas, J; Ovchinnikov, S; Lee, G; Wang, J; Cong, Q; Kinch, L; Schaeffer, R; Milln, C; Park, H; Adams, C; Glassman, C; Degiovanni, A; Pereira, J; Rodrigues, A; Dijk, Aav; Ebrecht, A; Opperman, D; Sagmeister, T; Buhlheller, C; Pavkov-Keller, T; Rathinaswamy, M; Dalwadi, U; Yip, C; Burke, J; Garcia, K; Grishin, N; Adams, P; Read, R; Baker, D; Bahi, M

Year: 2022

DOI: https://doi.org/10.1017/qrd.2022.12.pr3

Paper Identification of probable inhibitors for the DNA polymerase of the Monkeypox virus through the virtual screening approach.

Kumari, Swati; Chakraborty, Sayan; Ahmad, Mohammed et al. · 2023 · International journal of biological macromolecules · DOI

Full title: Identification of probable inhibitors for the DNA polymerase of the Monkeypox virus through the virtual screening approach.

Authors: Kumari, Swati; Chakraborty, Sayan; Ahmad, Mohammed; Kumar, Varun; Tailor, Prafullakumar B; Biswal, Bichitra K

Year: 2023

Venue: International journal of biological macromolecules

DOI: https://doi.org/10.1016/j.ijbiomac.2022.12.252

Paper Binding affinity between coronavirus spike protein and human ACE2 receptor

Shum, Marcus Ho-Hin; Lee, Yang; Tam, Leighton et al. · 2024 · Computational and Structural Biotechnology Journal · DOI

Full title: Binding affinity between coronavirus spike protein and human ACE2 receptor

Authors: Shum, Marcus Ho-Hin; Lee, Yang; Tam, Leighton; Xia, Hui; Chung, Lung Wa; Guo, Zhihong; Lam, Tommy Tsan‐Yuk

Year: 2024

Venue: Computational and Structural Biotechnology Journal

DOI: https://doi.org/10.1016/j.csbj.2024.01.009

Paper AlphaFold illuminates half of the dark human proteins.

Jessica L. Binder; J. Berendzen; Amy O. Stevens et al. · 2022 · Current Opinion in Structural Biology · DOI

Full title: AlphaFold illuminates half of the dark human proteins.

Authors: Jessica L. Binder; J. Berendzen; Amy O. Stevens; Yi He; Jian Wang; N. Dokholyan; Tudor I. Oprea

Year: 2022

Venue: Current Opinion in Structural Biology

DOI: https://doi.org/10.1016/j.sbi.2022.102372

Paper A Structure-Based Approach for Predicting Odor Similarity of Molecules via Docking Simulations with Human Olfactory Receptors

Kaneshiro, Hirotada; Sato, Masakazu; Tanaka, Airi et al. · 2025 · ACS Omega · DOI

Full title: A Structure-Based Approach for Predicting Odor Similarity of Molecules via Docking Simulations with Human Olfactory Receptors

Authors: Kaneshiro, Hirotada; Sato, Masakazu; Tanaka, Airi; Nakata, Shuya; Aihara, Yoshiko; Kitoh‐Nishioka, Hirotaka; Mori, Y.; Tanaka, Shigenori

Year: 2025

Venue: ACS Omega

DOI: https://doi.org/10.1021/acsomega.5c04324

Paper RAPID-Net: Accurate Pocket Identification for Binding-Site-Agnostic Docking.

Balytskyi, Yaroslav; Hubenko, Inna; Balytska, Alina et al. · 2025 · Journal of chemical information and modeling · DOI

Full title: RAPID-Net: Accurate Pocket Identification for Binding-Site-Agnostic Docking.

Authors: Balytskyi, Yaroslav; Hubenko, Inna; Balytska, Alina; Kelly, Christopher V

Year: 2025

Venue: Journal of chemical information and modeling

DOI: https://doi.org/10.1021/acs.jcim.5c01744

Paper Structure-Based Drug Design with a Deep Hierarchical Generative Model.

Weller, Jesse A; Rohs, Remo · 2024 · Journal of chemical information and modeling · DOI

Full title: Structure-Based Drug Design with a Deep Hierarchical Generative Model.

Authors: Weller, Jesse A; Rohs, Remo

Year: 2024

Venue: Journal of chemical information and modeling

DOI: https://doi.org/10.1021/acs.jcim.4c01193

Paper ‘Druggability’ of the Per–Arnt–Sim (PAS) domains of human PAS domain kinase, a therapeutic target for metabolic and liver disorders

Xu, Shangze; Fan, Lanyu; Zaborniak, Piotr et al. · 2024 · QRB Discovery · DOI

Full title: ‘Druggability’ of the Per–Arnt–Sim (PAS) domains of human PAS domain kinase, a therapeutic target for metabolic and liver disorders

Authors: Xu, Shangze; Fan, Lanyu; Zaborniak, Piotr; Zhu, Ruidi; Ji, Haoyuan; Madden, Katrina S.; Souza, João Vicente Braga de; Bronowska, Agnieszka K.

Year: 2024

Venue: QRB Discovery

DOI: https://doi.org/10.1017/qrd.2024.1

Paper Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development

Nam, Kwangho; Shao, Yihan; Major, Dan Thomas et al. · 2024 · ACS Omega · DOI

Full title: Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development

Authors: Nam, Kwangho; Shao, Yihan; Major, Dan Thomas; Wolf‐Watz, Magnus

Year: 2024

Venue: ACS Omega

DOI: https://doi.org/10.1021/acsomega.3c09084

Paper Natural Product-Inspired Bis(trifluoromethyl) Phenyl Hydroxycinnamate Derivatives as Promising Nonsteroidal Inhibitors of Human Steroid 5α-Reductase Type-1: Synthesis, In Vitro, and In Silico Studies

Isswanich, Kulpornsorn; Poungcho, Pattara; Buaban, Koonchira et al. · 2025 · ACS Omega · DOI

Full title: Natural Product-Inspired Bis(trifluoromethyl) Phenyl Hydroxycinnamate Derivatives as Promising Nonsteroidal Inhibitors of Human Steroid 5α-Reductase Type-1: Synthesis, In Vitro, and In Silico Studies

Authors: Isswanich, Kulpornsorn; Poungcho, Pattara; Buaban, Koonchira; Chuntakaruk, Hathaichanok; Sanachai, Kamonpan; Chansriniyom, Chaisak; Rungrotmongkol, Thanyada; De‐Eknamkul, Wanchai; Chamni, Supakarn

Year: 2025

Venue: ACS Omega

DOI: https://doi.org/10.1021/acsomega.5c06242

Paper RAPID-Net: Accurate Pocket Identification for Binding-Site-AgnosticDocking

(21788116), Yaroslav Balytskyi, (22614437), Inna Hubenko, (22614440), Alina Balytska, (1293888), Christopher V. Kelly · 2025 · Figshare · DOI

Full title: RAPID-Net: Accurate Pocket Identification for Binding-Site-AgnosticDocking

Authors: (21788116), Yaroslav Balytskyi, (22614437), Inna Hubenko, (22614440), Alina Balytska, (1293888), Christopher V. Kelly

Year: 2025

Venue: Figshare

DOI: https://doi.org/10.1021/acs.jcim.5c01744.s001

Paper Discovery of Chemical Scaffolds as Lysophosphatidic Acid Receptor 1 Antagonists: Virtual Screening, In Vitro Validation, and Molecular Dynamics Analysis

Lan Phuong Nguyen; R. Khan; Soomin Kang et al. · 2023 · ACS Omega · DOI

Full title: Discovery of Chemical Scaffolds as Lysophosphatidic Acid Receptor 1 Antagonists: Virtual Screening, In Vitro Validation, and Molecular Dynamics Analysis

Authors: Lan Phuong Nguyen; R. Khan; Soomin Kang; Hobin Lee; Jong-Ik Hwang; Hong-Rae Kim

Year: 2023

Venue: ACS Omega

DOI: https://doi.org/10.1021/acsomega.3c04798

Paper Computational approaches streamlining drug discovery

Sadybekov, Anastasiia; Katritch, Vsevolod · 2023 · Nature · DOI

Full title: Computational approaches streamlining drug discovery

Authors: Sadybekov, Anastasiia; Katritch, Vsevolod

Year: 2023

Venue: Nature

DOI: https://doi.org/10.1038/s41586-023-05905-z

Paper CACHE (Critical Assessment of Computational Hit-finding Experiments): A public–private partnership benchmarking initiative to enable the development of computational methods for hit-finding

Ackloo, Suzanne; Al‐awar, Rima; Amaro, Rommie E. et al. · 2022 · Nature Reviews Chemistry · DOI

Full title: CACHE (Critical Assessment of Computational Hit-finding Experiments): A public–private partnership benchmarking initiative to enable the development of computational methods for hit-finding

Authors: Ackloo, Suzanne; Al‐awar, Rima; Amaro, Rommie E.; Arrowsmith, C.H.; Azevedo, Hatylas; Batey, Robert A.; Bengio, Yoshua; Betz, Ulrich A. K.; Bologa, Cristian; Chodera, John D.; Cornell, Wendy D.; Dunham, Ian; Ecker, Gerhard F.; Edfeldt, Kristina; Edwards, A.M.; Gilson, Michael K.; Gordijo, Cláudia R.; Heßler, Gerhard; Hillisch, Alexander; Hogner, Anders; Irwin, John J.; Jansen, Johanna M.; Kühn, Daniel; Leach, Andrew R.; Lee, Alpha A.; Lessel, Uta; Morgan, Maxwell R.; Moult, John; Muegge, Ingo; Oprea, Tudor I.; Perry, Benjamin; Riley, Patrick; Rousseaux, Sophie A. L.; Saikatendu, Kumar Singh; Santhakumar, Vijayaratnam; Schapira, Matthieu; Scholten, Cora; Todd, Matthew H.; Vedadi, Masoud; Volkamer, Andrea; Willson, Timothy M.

Year: 2022

Venue: Nature Reviews Chemistry

DOI: https://doi.org/10.1038/s41570-022-00363-z

Paper AI is a viable alternative to high throughput screening: a 318-target study

Wallach, Izhar; Bernard, Denzil; Nguyen, Kong T. et al. · 2024 · Scientific Reports · DOI

Full title: AI is a viable alternative to high throughput screening: a 318-target study

Authors: Wallach, Izhar; Bernard, Denzil; Nguyen, Kong T.; Ho, Gregory; Morrison, Adrian R.; Stecuła, Adrian; Rosnik, Andreana M.; O’Sullivan, Ann; Davtyan, Aram; Samudio, Ben; Thomas, Bill; Worley, Brad; Butler, Brittany; Laggner, Christian; Thayer, Desiree A.; Moharreri, Ehsan; Friedland, Greg; Truong, Ha H.; Bedem, Henry van den; Ng, Ho Leung; Stafford, Kate A.; Sarangapani, Krishna K.; Giesler, Kyle; Ngo, Lien; Mysinger, Michael M.; Ahmed, Mostafa; Anthis, Nicholas J.; Henriksen, Niel M.; Gniewek, Paweł; Eckert, S.R.; Oliveira, Saulo de; Suterwala, Shabbir; PrasadPrasad, Srimukh Veccham Krishna; Shek, Stefani; Contreras, Stephanie; Hare, Stephanie R.; Palazzo, Teresa A.; O’Brien, Terrence E.; Grack, Tessa Van; Williams, Tiffany R.; Chern, Ting‐Rong; Kenyon, Victor; Lee, Andreia H.; Cann, Andrew B.; Bergman, Bastiaan; Anderson, Brandon; Cox, Bryan D.; Warrington, Jeffrey M.; Sorenson, Jon M.; Goldenberg, Joshua M.; Young, Matthew A.; DeHaan, Nicholas; Pemberton, Ryan P.; Schroedl, Stefan; Abramyan, Tigran M.; Gupta, T. Raghavendra; Mysore, Venkatesh; Presser, Adam; Ferrando, Adolfo A.; Andricopulo, Adriano D.; Ghosh, Agnidipta; Ayachi, Aicha Gharbi; Mushtaq, Aisha; Shaqra, Ala M.; Toh, Alan Kie Leong; Smrcka, Alan V.; Ciccia, Alberto; Oliveira, Aldo Sena de; Sverzhinsky, Aleksandr; Sousa, Alessandra Mara de; Agoulnik, Alexander I.; Kushnir, Alexander; Freiberg, Alexander N.; Statsyuk, Alexander V.; Gingras, Alexandre R.; Degterev, Alexei; Tomilov, Alexey; Vrielink, Alice; Garaeva, Alisa A.; Bryant-Friedrich, Amanda; Caflisch, Amedeo; Patel, Amit K.; Rangarajan, Amith Vikram; Matheeussen, An; Battistoni, Andrea; Caporali, Andrea; Chini, Andrea; Ilari, Andrea; Mattevi, Andrea; Foote, Andrea; Trabocchi, Andrea; Stahl, Andreas; Herr, Andrew B.; Berti, Andrew D.; Freywald, Andrew; Reidenbach, Andrew G.; Lam, Andrew; Cuddihy, Andrew; White, Andrew D.; Taglialatela, Angelo

Year: 2024

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-024-54655-z

Paper A highly accurate metadynamics-based Dissociation Free Energy method to calculate protein–protein and protein–ligand binding potencies

Wang, Jing; Ishchenko, Alexey; Zhang, Wei et al. · 2022 · Scientific Reports · DOI

Full title: A highly accurate metadynamics-based Dissociation Free Energy method to calculate protein–protein and protein–ligand binding potencies

Authors: Wang, Jing; Ishchenko, Alexey; Zhang, Wei; Razavi, Asghar M.; Langley, David R.

Year: 2022

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-022-05875-8

Paper Computational biology assisted exploration of phytochemicals derived natural inhibitors to block BZLF1 gene activation of Epstein–Bar virus in host

Naveed, Muhammad; Hussain, Muzamal; Aziz, Tariq et al. · 2024 · Scientific Reports · DOI

Full title: Computational biology assisted exploration of phytochemicals derived natural inhibitors to block BZLF1 gene activation of Epstein–Bar virus in host

Authors: Naveed, Muhammad; Hussain, Muzamal; Aziz, Tariq; Hanif, Nimra; Kanwal, Nazia; Arshad, Arooj; Khan, Ayaz Ali; Alshammari, Abdulrahman; Alharbi, Metab

Year: 2024

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-024-81037-2

Paper Inferring molecular inhibition potency with AlphaFold predicted structures

Oliveira, Pedro F.; Guedes, Rita C.; Falcão, André O. · 2024 · Scientific Reports · DOI

Full title: Inferring molecular inhibition potency with AlphaFold predicted structures

Authors: Oliveira, Pedro F.; Guedes, Rita C.; Falcão, André O.

Year: 2024

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-024-58394-z

Paper Augmented BindingNet dataset for enhanced ligand binding pose predictions using deep learning

Zhu, Hui; Li, Xuelian; Chen, Baoquan et al. · 2025 · npj Drug Discovery. · DOI

Full title: Augmented BindingNet dataset for enhanced ligand binding pose predictions using deep learning

Authors: Zhu, Hui; Li, Xuelian; Chen, Baoquan; Huang, Niu

Year: 2025

Venue: npj Drug Discovery.

DOI: https://doi.org/10.1038/s44386-024-00003-0

Paper Accelerating drug discovery for Disease X via an AlphaFold2 driven drug repositioning strategy

Zhao, Huijian, Qi, Wentao, Liu, Kebin, Zhao, Jiayi, Hu, Xueping, Deng, Wei · 2025 · Physical Chemistry Chemical Physics · DOI

Full title: Accelerating drug discovery for Disease X via an AlphaFold2 driven drug repositioning strategy

Authors: Zhao, Huijian, Qi, Wentao, Liu, Kebin, Zhao, Jiayi, Hu, Xueping, Deng, Wei

Year: 2025

Venue: Physical Chemistry Chemical Physics

DOI: https://doi.org/10.1039/d5cp01365h

Paper A chronotherapeutics-applicable multi-target therapeutics based on AI: Example of therapeutic hypothermia

Liu, Fei, Jiang, Xiangkang, Yang, Jingyuan, Tao, Jiawei, Zhang, Mao · 2022 · Briefings in Bioinformatics · DOI

Full title: A chronotherapeutics-applicable multi-target therapeutics based on AI: Example of therapeutic hypothermia

Authors: Liu, Fei, Jiang, Xiangkang, Yang, Jingyuan, Tao, Jiawei, Zhang, Mao

Year: 2022

Venue: Briefings in Bioinformatics

DOI: https://doi.org/10.1093/bib/bbac365

Paper Deep learning guided high-throughput virtual screening for in vitro antibody maturation

Chen, Gong; Liu, Hongde · 2025 · BIO Web of Conferences · DOI

Full title: Deep learning guided high-throughput virtual screening for in vitro antibody maturation

Authors: Chen, Gong; Liu, Hongde

Year: 2025

Venue: BIO Web of Conferences

DOI: https://doi.org/10.1051/bioconf/202517403017

Paper AI in drug design: evolution or revolution?

Green, Darren V. S. · 2025 · Emerging Topics in Life Sciences · DOI

Full title: AI in drug design: evolution or revolution?

Authors: Green, Darren V. S.

Year: 2025

Venue: Emerging Topics in Life Sciences

DOI: https://doi.org/10.1042/etls20240005

Paper Computational methods directed towards drug repurposing for COVID-19: advantages and limitations

Sharma, Prem P.; Bansal, Meenakshi; Sethi, Aaftaab et al. · 2021 · RSC Advances · DOI

Full title: Computational methods directed towards drug repurposing for COVID-19: advantages and limitations

Authors: Sharma, Prem P.; Bansal, Meenakshi; Sethi, Aaftaab; Poonam, Poonam; Pena, Lindomar; Goel, Vijay Kumar; Grishina, Maria; Chaturvedi, Shubhra; Kumar, Dhruv; Rathi, Brijesh

Year: 2021

Venue: RSC Advances

DOI: https://doi.org/10.1039/d1ra05320e

Paper The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies

Waman, Vaishali; Sen, Neeladri; Váradi, Mihály et al. · 2020 · Briefings in Bioinformatics · DOI

Full title: The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies

Authors: Waman, Vaishali; Sen, Neeladri; Váradi, Mihály; Daina, Antoine; Wodak, Shoshana J.; Zoete, Vincent; Velankar, Sameer; Orengo, Christine

Year: 2020

Venue: Briefings in Bioinformatics

DOI: https://doi.org/10.1093/bib/bbaa362

Paper Artificial Intelligence-based database for prediction of protein structure and their alterations in ocular diseases

Cen, Ling‐Ping; Ng, Tsz Kin; Ji, Jie et al. · 2023 · Database · DOI

Full title: Artificial Intelligence-based database for prediction of protein structure and their alterations in ocular diseases

Authors: Cen, Ling‐Ping; Ng, Tsz Kin; Ji, Jie; Lin, Jianwei; Yao, Yao; Yang, Rucui; Dong, Geng; Cao, Yingjie; Chen, Chong‐Bo; Yao, Shiqi; Wang, Wenying; Huang, Zijing; Qiu, Kunliang; Pang, Chi Pui; Liu, Qingping; Zhang, Mingzhi

Year: 2023

Venue: Database

DOI: https://doi.org/10.1093/database/baad083

Paper Pocket to concavity: a tool for the refinement of protein–ligand binding site shape from alpha spheres

Kudo, Genki; Hirao, Takumi; Yoshino, Ryunosuke et al. · 2023 · Bioinformatics · DOI

Full title: Pocket to concavity: a tool for the refinement of protein–ligand binding site shape from alpha spheres

Authors: Kudo, Genki; Hirao, Takumi; Yoshino, Ryunosuke; Shigeta, Yasuteru; Hirokawa, Takatsugu

Year: 2023

Venue: Bioinformatics

DOI: https://doi.org/10.1093/bioinformatics/btad212

Paper PredictONCO: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning

Štourač, Jan; Borko, Simeon; Khan, Rayyan Tariq et al. · 2023 · Briefings in Bioinformatics · DOI

Full title: PredictONCO: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning

Authors: Štourač, Jan; Borko, Simeon; Khan, Rayyan Tariq; Pokorná, Petra; Dobias, Adam; Planas-Iglesias, Joan; Mazurenko, Stanislav; Pinto, Gaspar; Szotkowská, Veronika; Štěrba, Jaroslav; Slabý, Ondřej; Damborský, Jiřı́; Bednář, David

Year: 2023

Venue: Briefings in Bioinformatics

DOI: https://doi.org/10.1093/bib/bbad441

Paper Structure-guided computational insecticide discovery targeting β-N-acetyl-D-hexosaminidase of Ostrinia furnacalis.

Tahir, Adeena; Siddiqi, Abdul Rauf; Maryam, Arooma et al. · 2024 · Journal of biomolecular structure & dynamics · DOI

Full title: Structure-guided computational insecticide discovery targeting β-N-acetyl-D-hexosaminidase of Ostrinia furnacalis.

Authors: Tahir, Adeena; Siddiqi, Abdul Rauf; Maryam, Arooma; Chaitanya Vedithi, Sundeep; Blundell, Tom L

Year: 2024

Venue: Journal of biomolecular structure & dynamics

DOI: https://doi.org/10.1080/07391102.2023.2264394

Paper MulinforCPI: enhancing precision of compound–protein interaction prediction through novel perspectives on multi-level information integration

Nguyen, Ngoc-Quang, Park, Sejeong, Gim, Mogan, Kang, Jaewoo · 2023 · Briefings in Bioinformatics · DOI

Full title: MulinforCPI: enhancing precision of compound–protein interaction prediction through novel perspectives on multi-level information integration

Authors: Nguyen, Ngoc-Quang, Park, Sejeong, Gim, Mogan, Kang, Jaewoo

Year: 2023

Venue: Briefings in Bioinformatics

DOI: https://doi.org/10.1093/bib/bbad484

Paper A new paradigm for applying deep learning to protein–ligand interaction prediction

Wang, Zechen; Wang, Sheng; Li, Yangyang et al. · 2024 · Briefings in Bioinformatics · DOI

Full title: A new paradigm for applying deep learning to protein–ligand interaction prediction

Authors: Wang, Zechen; Wang, Sheng; Li, Yangyang; Guo, Jingjing; Wei, Yanjie; Mu, Yuguang; Zheng, Liangzhen; Li, Weifeng

Year: 2024

Venue: Briefings in Bioinformatics

DOI: https://doi.org/10.1093/bib/bbae145

Paper Guided docking as a data generation approach facilitates structure-based machine learning on kinases

Backenköhler, Michael; Groß, Joschka; Wolf, Verena et al. · 2023 · DOI

Full title: Guided docking as a data generation approach facilitates structure-based machine learning on kinases

Authors: Backenköhler, Michael; Groß, Joschka; Wolf, Verena; Volkamer, Andrea

Year: 2023

DOI: https://doi.org/10.26434/chemrxiv-2023-prk53

Paper Utilization of an Optimized AlphaFold Protein Model for Structure-Based Design of a Selective HDAC11 Inhibitor with Anti-neuroblastoma Activity

Baselious, Fady; Hilscher, Sebastian; Hagemann, Sven et al. · 2024 · DOI

Full title: Utilization of an Optimized AlphaFold Protein Model for Structure-Based Design of a Selective HDAC11 Inhibitor with Anti-neuroblastoma Activity

Authors: Baselious, Fady; Hilscher, Sebastian; Hagemann, Sven; Tripathee, Sunita; Robaa, Dina; Bařinka, Cyril; Hüttelmaier, Stefan; Schutkowski, Mike; Sippl, Wolfgang

Year: 2024

DOI: https://doi.org/10.26434/chemrxiv-2024-6f790

Paper AlphaFold meets de novo drug design: leveraging structural protein information in multi-target molecular generative models

Bernatavicius, Andrius, Šícho, Martin, Janssen, Antonius P. A., Hassen, Alan Kai, Preuß, Mike, Westen, Gerard J. P. van · 2024 · DOI

Full title: AlphaFold meets de novo drug design: leveraging structural protein information in multi-target molecular generative models

Authors: Bernatavicius, Andrius, Šícho, Martin, Janssen, Antonius P. A., Hassen, Alan Kai, Preuß, Mike, Westen, Gerard J. P. van

Year: 2024

DOI: https://doi.org/10.26434/chemrxiv-2024-60tc7-v2

Paper Docking-informed machine learning for kinome wide affinity prediction

Schifferstein, Jordy; Bernatavicius, Andrius; Janssen, Antonius P. A. · 2024 · DOI

Full title: Docking-informed machine learning for kinome wide affinity prediction

Authors: Schifferstein, Jordy; Bernatavicius, Andrius; Janssen, Antonius P. A.

Year: 2024

DOI: https://doi.org/10.26434/chemrxiv-2024-46rxl

Paper Deep Learning Strategies for Enhanced Molecular Docking and Virtual Screening

Silva, Matheus Müller Pereira da; Guedes, Isabella Alvim; Custódio, Fábio Lima et al. · 2023 · DOI

Full title: Deep Learning Strategies for Enhanced Molecular Docking and Virtual Screening

Authors: Silva, Matheus Müller Pereira da; Guedes, Isabella Alvim; Custódio, Fábio Lima; Krempser, Eduardo; Dardenne, Laurent E.

Year: 2023

DOI: https://doi.org/10.26434/chemrxiv-2023-zfv87-v2

Paper AlphaFold meets de novo drug design: leveraging structural protein information in multi-target molecular generative models

Bernatavicius, Andrius, Šícho, Martin, Janssen, Antonius P. A., Hassen, Alan Kai, Preuß, Mike, Westen, Gerard J. P. van · 2024 · DOI

Full title: AlphaFold meets de novo drug design: leveraging structural protein information in multi-target molecular generative models

Authors: Bernatavicius, Andrius, Šícho, Martin, Janssen, Antonius P. A., Hassen, Alan Kai, Preuß, Mike, Westen, Gerard J. P. van

Year: 2024

DOI: https://doi.org/10.26434/chemrxiv-2024-60tc7

Paper Applications of artificial intelligence and machine learning in pharmaceutical domain: A comprehensive review

Arivanantham, Sathishkumar, Sekar, Praveen, Sundhararajan, Naveena, Nagalingam, Yogadharshini, Raju, Senthil Kumar · 2023 · World Journal of Biology Pharmacy and Health Sciences · DOI

Full title: Applications of artificial intelligence and machine learning in pharmaceutical domain: A comprehensive review

Authors: Arivanantham, Sathishkumar, Sekar, Praveen, Sundhararajan, Naveena, Nagalingam, Yogadharshini, Raju, Senthil Kumar

Year: 2023

Venue: World Journal of Biology Pharmacy and Health Sciences

DOI: https://doi.org/10.30574/wjbphs.2023.16.2.0467

Paper İLAÇ TASARIMINDA YAPAY ZEKÂ UYGULAMALARI

TARI, Özden, ARPACI, Nuray · 2023 · Ankara Universitesi Eczacilik Fakultesi Dergisi · DOI

Full title: İLAÇ TASARIMINDA YAPAY ZEKÂ UYGULAMALARI

Authors: TARI, Özden, ARPACI, Nuray

Year: 2023

Venue: Ankara Universitesi Eczacilik Fakultesi Dergisi

DOI: https://doi.org/10.33483/jfpau.1327078

Paper Application of vision transformers to protein-ligand affinity prediction.

Poziemski, Jakub, Siedlecki, Paweł · 2025 · DOI

Full title: Application of vision transformers to protein-ligand affinity prediction.

Authors: Poziemski, Jakub, Siedlecki, Paweł

Year: 2025

DOI: https://doi.org/10.26434/chemrxiv-2025-qcxq1

Paper The use of machine learning-based sequential virtual screening in the search of new ligands of 5-HT6 receptor

Michał Sapa; Alicja Gawalska; M. Kołaczkowski et al. · 2023 · Farmacja polska · DOI

Full title: The use of machine learning-based sequential virtual screening in the search of new ligands of 5-HT6 receptor

Authors: Michał Sapa; Alicja Gawalska; M. Kołaczkowski; Adam Bucki

Year: 2023

Venue: Farmacja polska

DOI: https://doi.org/10.32383/farmpol/161474

Paper Structure-Guided Computational Approaches to Unravel Druggable Proteomic Landscape of Mycobacterium leprae

Vedithi, Sundeep Chaitanya; Malhotra, Sony; Acebrón-García-de-Eulate, Marta et al. · 2021 · Frontiers in Molecular Biosciences · DOI

Full title: Structure-Guided Computational Approaches to Unravel Druggable Proteomic Landscape of Mycobacterium leprae

Authors: Vedithi, Sundeep Chaitanya; Malhotra, Sony; Acebrón-García-de-Eulate, Marta; Matusevicius, Modestas; Torres, Pedro Henrique Monteiro; Blundell, Tom L.

Year: 2021

Venue: Frontiers in Molecular Biosciences

DOI: https://doi.org/10.3389/fmolb.2021.663301

Paper The Use of AlphaFold for In Silico Exploration of Drug Targets in the Parasite Trypanosoma cruzi

Ros-Lucas, Albert; Martínez-Peinado, Nieves; Bastida, Jaume et al. · 2022 · Frontiers in Cellular and Infection Microbiology · DOI

Full title: The Use of AlphaFold for In Silico Exploration of Drug Targets in the Parasite Trypanosoma cruzi

Authors: Ros-Lucas, Albert; Martínez-Peinado, Nieves; Bastida, Jaume; Gascón, Joaquím; Alonso-Padilla, Julio

Year: 2022

Venue: Frontiers in Cellular and Infection Microbiology

DOI: https://doi.org/10.3389/fcimb.2022.944748

Paper NeuralDock: Rapid and Conformation-Agnostic Docking of Small Molecules

Sha, Congzhou M.; Wang, Jian; Dokholyan, Nikolay V. · 2022 · Frontiers in Molecular Biosciences · DOI

Full title: NeuralDock: Rapid and Conformation-Agnostic Docking of Small Molecules

Authors: Sha, Congzhou M.; Wang, Jian; Dokholyan, Nikolay V.

Year: 2022

Venue: Frontiers in Molecular Biosciences

DOI: https://doi.org/10.3389/fmolb.2022.867241

Paper Essential Dynamics Ensemble Docking for Structure-Based GPCR Drug Discovery

McKay, Kyle T.; Hamilton, Nicholas B.; Remington, Jacob M. et al. · 2022 · Frontiers in Molecular Biosciences · DOI

Full title: Essential Dynamics Ensemble Docking for Structure-Based GPCR Drug Discovery

Authors: McKay, Kyle T.; Hamilton, Nicholas B.; Remington, Jacob M.; Schneebeli, Severin T.; Li, Jianing

Year: 2022

Venue: Frontiers in Molecular Biosciences

DOI: https://doi.org/10.3389/fmolb.2022.879212

Paper Discovery of a cryptic pocket in the AI-predicted structure of PPM1D phosphatase explains the binding site and potency of its allosteric inhibitors.

Meller, Artur; De Oliveira, Saulo; Davtyan, Aram et al. · 2023 · Frontiers in molecular biosciences · DOI

Full title: Discovery of a cryptic pocket in the AI-predicted structure of PPM1D phosphatase explains the binding site and potency of its allosteric inhibitors.

Authors: Meller, Artur; De Oliveira, Saulo; Davtyan, Aram; Abramyan, Tigran; Bowman, Gregory R; van den Bedem, Henry

Year: 2023

Venue: Frontiers in molecular biosciences

DOI: https://doi.org/10.3389/fmolb.2023.1171143

Paper Structural modeling of antibody variable regions using deep learning—progress and perspectives on drug discovery

Jaszczyszyn, Igor; Bielska, Weronika; Gawłowski, Tomasz et al. · 2023 · Frontiers in Molecular Biosciences · DOI

Full title: Structural modeling of antibody variable regions using deep learning—progress and perspectives on drug discovery

Authors: Jaszczyszyn, Igor; Bielska, Weronika; Gawłowski, Tomasz; Dudzic, Paweł; Satława, Tadeusz; Kończak, Jarosław; Wilman, Wiktoria; Janusz, Bartosz; Wróbel, Sonia; Chomicz, Dawid; Galson, Jacob D.; Leem, Jinwoo; Kelm, Sebastian; Krawczyk, Konrad

Year: 2023

Venue: Frontiers in Molecular Biosciences

DOI: https://doi.org/10.3389/fmolb.2023.1214424

Paper Recent Progress in Antibody Epitope Prediction

Zeng, Xincheng; Bai, Ganggang; Sun, Chuance et al. · 2023 · Antibodies · DOI

Full title: Recent Progress in Antibody Epitope Prediction

Authors: Zeng, Xincheng; Bai, Ganggang; Sun, Chuance; Ma, Buyong

Year: 2023

Venue: Antibodies

DOI: https://doi.org/10.3390/antib12030052

Paper Predicting the Assembly of the Transmembrane Domains of Viral Channel Forming Proteins and Peptide Drug Screening Using a Docking Approach

Huang, Ta-Chou; Fischer, Wolfgang B. · 2022 · Biomolecules · DOI

Full title: Predicting the Assembly of the Transmembrane Domains of Viral Channel Forming Proteins and Peptide Drug Screening Using a Docking Approach

Authors: Huang, Ta-Chou; Fischer, Wolfgang B.

Year: 2022

Venue: Biomolecules

DOI: https://doi.org/10.3390/biom12121844

Paper Multitasking Na+/Taurocholate Cotransporting Polypeptide (NTCP) as a Drug Target for HBV Infection: From Protein Engineering to Drug Discovery

Zakrzewicz, Dariusz; Geyer, Joachim · 2022 · Biomedicines · DOI

Full title: Multitasking Na+/Taurocholate Cotransporting Polypeptide (NTCP) as a Drug Target for HBV Infection: From Protein Engineering to Drug Discovery

Authors: Zakrzewicz, Dariusz; Geyer, Joachim

Year: 2022

Venue: Biomedicines

DOI: https://doi.org/10.3390/biomedicines10010196

Paper Conjecturing about Small-Molecule Agonists and Antagonists of α4β1 Integrin: From Mechanistic Insight to Potential Therapeutic Applications

He, Tingting; Giacomini, Daria; Tolomelli, Alessandra et al. · 2024 · Biomedicines · DOI

Full title: Conjecturing about Small-Molecule Agonists and Antagonists of α4β1 Integrin: From Mechanistic Insight to Potential Therapeutic Applications

Authors: He, Tingting; Giacomini, Daria; Tolomelli, Alessandra; Baiula, Monica; Gentilucci, Luca

Year: 2024

Venue: Biomedicines

DOI: https://doi.org/10.3390/biomedicines12020316

Paper Discovery and Characterization of Two Selective Inhibitors for a Mu-Class Glutathione S-Transferase of 25 kDa from Taenia solium Using Computational and Bioinformatics Tools.

Sánchez-Juárez, César; Flores-López, Roberto; Sánchez-Pérez, Lluvia de Carolina et al. · 2024 · Biomolecules · DOI

Full title: Discovery and Characterization of Two Selective Inhibitors for a Mu-Class Glutathione S-Transferase of 25 kDa from Taenia solium Using Computational and Bioinformatics Tools.

Authors: Sánchez-Juárez, César; Flores-López, Roberto; Sánchez-Pérez, Lluvia de Carolina; García-Gutiérrez, Ponciano; Jiménez, Lucía; Landa, Abraham; Zubillaga, Rafael A

Year: 2024

Venue: Biomolecules

DOI: https://doi.org/10.3390/biom15010007

Paper Evaluation of Myocilin Variant Protein Structures Modeled by AlphaFold2

Ng, Tsz Kin; Ji, Jie; Liu, Qingping et al. · 2023 · Biomolecules · DOI

Full title: Evaluation of Myocilin Variant Protein Structures Modeled by AlphaFold2

Authors: Ng, Tsz Kin; Ji, Jie; Liu, Qingping; Yao, Yao; Wang, Wenying; Cao, Yingjie; Chen, Chong‐Bo; Lin, Jianwei; Dong, Geng; Cen, Ling‐Ping; Huang, Chukai; Zhang, Mingzhi

Year: 2023

Venue: Biomolecules

DOI: https://doi.org/10.3390/biom14010014

Paper Conformational Dynamics of the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein

Мамчур, А. А.; Stanishneva-Konovalova, T.B.; Mokrushina, Yuliana A. et al. · 2022 · Biomedicines · DOI

Full title: Conformational Dynamics of the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein

Authors: Мамчур, А. А.; Stanishneva-Konovalova, T.B.; Mokrushina, Yuliana A.; Abrikosova, Viktoria A.; Guo, Yu; Zhang, Hongkai; Terekhov, Stanislav S.; Smirnov, I. V.; Yaroshevich, Igor A.

Year: 2022

Venue: Biomedicines

DOI: https://doi.org/10.3390/biomedicines10123233

Paper Using AlphaFold Predictions in Viral Research

Gutnik, Daria; Evseev, Peter V.; Miroshnikov, Konstantin A. et al. · 2023 · Current Issues in Molecular Biology · DOI

Full title: Using AlphaFold Predictions in Viral Research

Authors: Gutnik, Daria; Evseev, Peter V.; Miroshnikov, Konstantin A.; Shneider, Mikhail M.

Year: 2023

Venue: Current Issues in Molecular Biology

DOI: https://doi.org/10.3390/cimb45040240

Paper Artificial Intelligence in Aptamer–Target Binding Prediction

Chen, Zihao; Hu, Long; Zhang, Bao‐Ting et al. · 2021 · International Journal of Molecular Sciences · DOI

Full title: Artificial Intelligence in Aptamer–Target Binding Prediction

Authors: Chen, Zihao; Hu, Long; Zhang, Bao‐Ting; Lü, Aiping; Wang, Yaofeng; Yu, Yuanyuan; Zhang, Ge

Year: 2021

Venue: International Journal of Molecular Sciences

DOI: https://doi.org/10.3390/ijms22073605

Paper Machine Learning Assisted Approach for Finding Novel High Activity Agonists of Human Ectopic Olfactory Receptors

Jabeen, Amara; March, Claire A. de; Matsunami, Hiroaki et al. · 2021 · International Journal of Molecular Sciences · DOI

Full title: Machine Learning Assisted Approach for Finding Novel High Activity Agonists of Human Ectopic Olfactory Receptors

Authors: Jabeen, Amara; March, Claire A. de; Matsunami, Hiroaki; Ranganathan, Shoba

Year: 2021

Venue: International Journal of Molecular Sciences

DOI: https://doi.org/10.3390/ijms222111546

Paper A Comprehensive Mapping of the Druggable Cavities within the SARS-CoV-2 Therapeutically Relevant Proteins by Combining Pocket and Docking Searches as Implemented in Pockets 2.0

Gervasoni, Silvia; Vistoli, Giulio; Talarico, Carmine et al. · 2020 · International Journal of Molecular Sciences · DOI

Full title: A Comprehensive Mapping of the Druggable Cavities within the SARS-CoV-2 Therapeutically Relevant Proteins by Combining Pocket and Docking Searches as Implemented in Pockets 2.0

Authors: Gervasoni, Silvia; Vistoli, Giulio; Talarico, Carmine; Manelfi, Candida; Beccari, Andrea R.; Studer, Gabriel; Tauriello, Gerardo; Waterhouse, Andrew; Schwede, Torsten; Pedretti, Alessandro

Year: 2020

Venue: International Journal of Molecular Sciences

DOI: https://doi.org/10.3390/ijms21145152

Paper Structure Prediction, Evaluation, and Validation of GPR18 Lipid Receptor Using Free Programs

Michalik, Ilona; Kuder, Kamil; Kieć‐Kononowicz, Katarzyna et al. · 2022 · International Journal of Molecular Sciences · DOI

Full title: Structure Prediction, Evaluation, and Validation of GPR18 Lipid Receptor Using Free Programs

Authors: Michalik, Ilona; Kuder, Kamil; Kieć‐Kononowicz, Katarzyna; Handzlik, Jadwiga

Year: 2022

Venue: International Journal of Molecular Sciences

DOI: https://doi.org/10.3390/ijms23147917

Paper Estimating the Similarity between Protein Pockets

Eguida, Merveille; Rognan, Didier · 2022 · International Journal of Molecular Sciences · DOI

Full title: Estimating the Similarity between Protein Pockets

Authors: Eguida, Merveille; Rognan, Didier

Year: 2022

Venue: International Journal of Molecular Sciences

DOI: https://doi.org/10.3390/ijms232012462

Paper Structural Modifications Introduced by NS2B Cofactor Binding to the NS3 Protease of the Kyasanur Forest Disease Virus.

Kandagalla, Shivananda; Kumbar, Bhimanagoud; Novak, Jurica · 2023 · International journal of molecular sciences · DOI

Full title: Structural Modifications Introduced by NS2B Cofactor Binding to the NS3 Protease of the Kyasanur Forest Disease Virus.

Authors: Kandagalla, Shivananda; Kumbar, Bhimanagoud; Novak, Jurica

Year: 2023

Venue: International journal of molecular sciences

DOI: https://doi.org/10.3390/ijms241310907

Paper Substrate Recognition Properties from an Intermediate Structural State of the UreA Transporter

Sanguinetti, Manuel; Santos, Lucianna Helene; Dourron, Juliette et al. · 2022 · International Journal of Molecular Sciences · DOI

Full title: Substrate Recognition Properties from an Intermediate Structural State of the UreA Transporter

Authors: Sanguinetti, Manuel; Santos, Lucianna Helene; Dourron, Juliette; Alamón, Catalina; Idiarte, Juan; Amillis, Sotiris; Pantano, Sergio; Ramón, Ana

Year: 2022

Venue: International Journal of Molecular Sciences

DOI: https://doi.org/10.3390/ijms232416039

Paper Identification of Potential Druggable Targets and Structure-Based Virtual Screening for Drug-like Molecules against the Shrimp Pathogen Enterocytozoon hepatopenaei

Paria, Prasenjit; Tassanakajon, Anchalee · 2023 · International Journal of Molecular Sciences · DOI

Full title: Identification of Potential Druggable Targets and Structure-Based Virtual Screening for Drug-like Molecules against the Shrimp Pathogen Enterocytozoon hepatopenaei

Authors: Paria, Prasenjit; Tassanakajon, Anchalee

Year: 2023

Venue: International Journal of Molecular Sciences

DOI: https://doi.org/10.3390/ijms24021412

Paper Pharmacoinformatic Investigation of Silymarin as a Potential Inhibitor against Nemopilema nomurai Jellyfish Metalloproteinase Toxin-like Protein

Asirvatham, Ravi Deva; Hwang, Du Hyeon; Prakash, Ramachandran Loganathan Mohan et al. · 2023 · International Journal of Molecular Sciences · DOI

Full title: Pharmacoinformatic Investigation of Silymarin as a Potential Inhibitor against Nemopilema nomurai Jellyfish Metalloproteinase Toxin-like Protein

Authors: Asirvatham, Ravi Deva; Hwang, Du Hyeon; Prakash, Ramachandran Loganathan Mohan; Kang, Changkeun; Kim, Euikyung

Year: 2023

Venue: International Journal of Molecular Sciences

DOI: https://doi.org/10.3390/ijms24108972

Paper Pharmacological Chaperones and Protein Conformational Diseases: Approaches of Computational Structural Biology

Grasso, Daniela; Galderisi, Silvia; Santucci, Annalisa et al. · 2023 · International Journal of Molecular Sciences · DOI

Full title: Pharmacological Chaperones and Protein Conformational Diseases: Approaches of Computational Structural Biology

Authors: Grasso, Daniela; Galderisi, Silvia; Santucci, Annalisa; Bernini, Andrea

Year: 2023

Venue: International Journal of Molecular Sciences

DOI: https://doi.org/10.3390/ijms24065819

Paper Identification of Catechins’ Binding Sites in Monomeric Aβ42 through Ensemble Docking and MD Simulations

Firouzi, Rohoullah; Sowlati‐Hashjin, Shahin; Chávez-García, Cecilia et al. · 2023 · International Journal of Molecular Sciences · DOI

Full title: Identification of Catechins’ Binding Sites in Monomeric Aβ42 through Ensemble Docking and MD Simulations

Authors: Firouzi, Rohoullah; Sowlati‐Hashjin, Shahin; Chávez-García, Cecilia; Ashouri, Mitra; Karimi‐Jafari, Mohammad Hossein; Karttunen, Mikko

Year: 2023

Venue: International Journal of Molecular Sciences

DOI: https://doi.org/10.3390/ijms24098161

Paper Inhibitor Trapping in N-Myristoyltransferases as a Mechanism for Drug Potency

Spassov, Danislav S.; Atanasova, Mariyana; Doytchinova, Irini · 2023 · International Journal of Molecular Sciences · DOI

Full title: Inhibitor Trapping in N-Myristoyltransferases as a Mechanism for Drug Potency

Authors: Spassov, Danislav S.; Atanasova, Mariyana; Doytchinova, Irini

Year: 2023

Venue: International Journal of Molecular Sciences

DOI: https://doi.org/10.3390/ijms241411610

Paper An Updated Review on Developing Small Molecule Kinase Inhibitors Using Computer-Aided Drug Design Approaches

Li, Linwei; Liu, Song‐Tao; Bi, Wang et al. · 2023 · International Journal of Molecular Sciences · DOI

Full title: An Updated Review on Developing Small Molecule Kinase Inhibitors Using Computer-Aided Drug Design Approaches

Authors: Li, Linwei; Liu, Song‐Tao; Bi, Wang; Liu, Fei; Xu, Shuhua; Li, Pirui; Chen, Yu

Year: 2023

Venue: International Journal of Molecular Sciences

DOI: https://doi.org/10.3390/ijms241813953

Paper Comparative Structure-Based Virtual Screening Utilizing Optimized AlphaFold Model Identifies Selective HDAC11 Inhibitor.

Baselious, Fady; Hilscher, Sebastian; Robaa, Dina et al. · 2024 · International journal of molecular sciences · DOI

Full title: Comparative Structure-Based Virtual Screening Utilizing Optimized AlphaFold Model Identifies Selective HDAC11 Inhibitor.

Authors: Baselious, Fady; Hilscher, Sebastian; Robaa, Dina; Barinka, Cyril; Schutkowski, Mike; Sippl, Wolfgang

Year: 2024

Venue: International journal of molecular sciences

DOI: https://doi.org/10.3390/ijms25021358

Paper Target Prediction by Multiple Virtual Screenings: Analyzing the SARS-CoV-2 Phenotypic Screening by the Docking Simulations Submitted to the MEDIATE Initiative

Gervasoni, Silvia; Manelfi, Candida; Adobati, Sara et al. · 2023 · International Journal of Molecular Sciences · DOI

Full title: Target Prediction by Multiple Virtual Screenings: Analyzing the SARS-CoV-2 Phenotypic Screening by the Docking Simulations Submitted to the MEDIATE Initiative

Authors: Gervasoni, Silvia; Manelfi, Candida; Adobati, Sara; Talarico, Carmine; Biswas, Akash Deep; Pedretti, Alessandro; Vistoli, Giulio; Beccari, Andrea R.

Year: 2023

Venue: International Journal of Molecular Sciences

DOI: https://doi.org/10.3390/ijms25010450

Paper Design of Cyclic Peptides Targeting Protein–Protein Interactions Using AlphaFold

Kosugi, Takatsugu; Ohue, Masahito · 2023 · International Journal of Molecular Sciences · DOI

Full title: Design of Cyclic Peptides Targeting Protein–Protein Interactions Using AlphaFold

Authors: Kosugi, Takatsugu; Ohue, Masahito

Year: 2023

Venue: International Journal of Molecular Sciences

DOI: https://doi.org/10.3390/ijms241713257

Paper Efficient Refinement of Complex Structures of Flexible Histone Peptides Using Post-Docking Molecular Dynamics Protocols

Bayarsaikhan, Bayartsetseg; Zsidó, Balázs Zoltán; Börzsei, Rita et al. · 2024 · International Journal of Molecular Sciences · DOI

Full title: Efficient Refinement of Complex Structures of Flexible Histone Peptides Using Post-Docking Molecular Dynamics Protocols

Authors: Bayarsaikhan, Bayartsetseg; Zsidó, Balázs Zoltán; Börzsei, Rita; Hetényi, Csaba

Year: 2024

Venue: International Journal of Molecular Sciences

DOI: https://doi.org/10.3390/ijms25115945

Paper Anopheles gambiae Trehalase Inhibitors for Malaria Vector Control: A Molecular Docking and Molecular Dynamics Study

Adedeji, Eunice O.; Oduselu, Gbolahan O.; Ogunlana, Olubanke Olujoke et al. · 2022 · Insects · DOI

Full title: Anopheles gambiae Trehalase Inhibitors for Malaria Vector Control: A Molecular Docking and Molecular Dynamics Study

Authors: Adedeji, Eunice O.; Oduselu, Gbolahan O.; Ogunlana, Olubanke Olujoke; Fatumo, Segun; Koenig, Rainer; Adebiyi, Ezekiel

Year: 2022

Venue: Insects

DOI: https://doi.org/10.3390/insects13111070

Paper Identifying Residues for Substrate Recognition in Human GPAT4 by Molecular Dynamics Simulations

Liu, Yulan; Xu, Yunong; Xu, Yinuo et al. · 2024 · International Journal of Molecular Sciences · DOI

Full title: Identifying Residues for Substrate Recognition in Human GPAT4 by Molecular Dynamics Simulations

Authors: Liu, Yulan; Xu, Yunong; Xu, Yinuo; Zhao, Zhihao; Cheng, Gui‐Juan; Ren, Ruobing; Chiang, Ying‐Chih

Year: 2024

Venue: International Journal of Molecular Sciences

DOI: https://doi.org/10.3390/ijms25073729

Paper P-Loop Channels: Experimental Structures, and Physics-Based and Neural Networks-Based Models

Tikhonov, Denis B.; Zhorov, Boris S. · 2022 · Membranes · DOI

Full title: P-Loop Channels: Experimental Structures, and Physics-Based and Neural Networks-Based Models

Authors: Tikhonov, Denis B.; Zhorov, Boris S.

Year: 2022

Venue: Membranes

DOI: https://doi.org/10.3390/membranes12020229

Paper Bioactive Phytoconstituents as Potent Inhibitors of Tyrosine-Protein Kinase Yes (YES1): Implications in Anticancer Therapeutics

Chun-Chieh Yang; A. Alam; F. Alhumaydhi et al. · 2022 · Molecules · DOI

Full title: Bioactive Phytoconstituents as Potent Inhibitors of Tyrosine-Protein Kinase Yes (YES1): Implications in Anticancer Therapeutics

Authors: Chun-Chieh Yang; A. Alam; F. Alhumaydhi; M. Khan; S. Alsagaby; Waleed Al Abdulmonem; M. Hassan; Anas Shamsi; B. Bano; D. Yadav

Year: 2022

Venue: Molecules

DOI: https://doi.org/10.3390/molecules27103060

Paper Drug Design: Where We Are and Future Prospects

Zagotto, Giuseppe; Bortoli, Marco · 2021 · Molecules · DOI

Full title: Drug Design: Where We Are and Future Prospects

Authors: Zagotto, Giuseppe; Bortoli, Marco

Year: 2021

Venue: Molecules

DOI: https://doi.org/10.3390/molecules26227061

Paper Protein–Ligand Docking in the Machine-Learning Era

Yang, Chao; Chen, Eric Anthony; Zhang, Yingkai · 2022 · Molecules · DOI

Full title: Protein–Ligand Docking in the Machine-Learning Era

Authors: Yang, Chao; Chen, Eric Anthony; Zhang, Yingkai

Year: 2022

Venue: Molecules

DOI: https://doi.org/10.3390/molecules27144568

Paper Application of Mathematical Modeling and Computational Tools in the Modern Drug Design and Development Process

Hasan, Md. Rifat; Alsaiari, Ahad Amer; Fakhurji, Burhan Zain et al. · 2022 · Molecules · DOI

Full title: Application of Mathematical Modeling and Computational Tools in the Modern Drug Design and Development Process

Authors: Hasan, Md. Rifat; Alsaiari, Ahad Amer; Fakhurji, Burhan Zain; Molla, Mohammad Habibur Rahman; Asseri, Amer H.; Sumon, Md Afsar Ahmed; Park, Moon Nyeo; Ahammad, Foysal; Kim, Bonglee

Year: 2022

Venue: Molecules

DOI: https://doi.org/10.3390/molecules27134169

Paper Neuropeptides, New Ligands of SARS-CoV-2 Nucleoprotein, a Potential Link between Replication, Inflammation and Neurotransmission

Henri, Julien; Minder, Lætitia; Mohanasundaram, Kevin et al. · 2022 · Molecules · DOI

Full title: Neuropeptides, New Ligands of SARS-CoV-2 Nucleoprotein, a Potential Link between Replication, Inflammation and Neurotransmission

Authors: Henri, Julien; Minder, Lætitia; Mohanasundaram, Kevin; Dilly, Sébastien; Lamy, Anne; Primo, Carmelo Di; Slama‐Schwok, Anny

Year: 2022

Venue: Molecules

DOI: https://doi.org/10.3390/molecules27228094

Paper Identification of Disalicyloyl Curcumin as a Potential DNA Polymerase Inhibitor for Marek’s Disease Herpesvirus: A Computational Study Using Virtual Screening and Molecular Dynamics Simulations

Aziza Cherif; Zarrin Basharat; Muhammad Yaseen et al. · 2023 · Molecules · DOI

Full title: Identification of Disalicyloyl Curcumin as a Potential DNA Polymerase Inhibitor for Marek’s Disease Herpesvirus: A Computational Study Using Virtual Screening and Molecular Dynamics Simulations

Authors: Aziza Cherif; Zarrin Basharat; Muhammad Yaseen; M. A. Bhat; Imad Uddin; Noha Ziedan; Fazal Mabood; N. Sadfi‐Zouaoui; Abdelmonaem Messaoudi

Year: 2023

Venue: Molecules

DOI: https://doi.org/10.3390/molecules28186576

Paper Solubilization, purification, and characterization of the hexameric form of phosphatidylserine synthase from Candida albicans

Zhou, Yue; Syed, Jawhar H.; Semchonok, Dmitry A. et al. · 2023 · Journal of Biological Chemistry · DOI

Full title: Solubilization, purification, and characterization of the hexameric form of phosphatidylserine synthase from Candida albicans

Authors: Zhou, Yue; Syed, Jawhar H.; Semchonok, Dmitry A.; Wright, Edward; Kyrilis, Fotis L.; Hamdi, Farzad; Kastritis, Panagiotis L.; Bruce, Barry D.; Reynolds, Todd B.

Year: 2023

Venue: Journal of Biological Chemistry

DOI: https://doi.org/10.1016/j.jbc.2023.104756

Paper Modeling the Orthosteric Binding Site of the G Protein-Coupled Odorant Receptor OR5K1

Nicoli, Alessandro; Haag, Franziska; Marcinek, Patrick et al. · 2022 · DOI

Full title: Modeling the Orthosteric Binding Site of the G Protein-Coupled Odorant Receptor OR5K1

Authors: Nicoli, Alessandro; Haag, Franziska; Marcinek, Patrick; He, Ruiming; Kreißl, Johanna; Stein, Jörg; Marchetto, Alessandro; Dunkel, Andreas; Hofmann, Thomas; Krautwurst, Dietmar; Pizio, Antonella Di

Year: 2022

DOI: https://doi.org/10.1101/2022.06.01.494157

Paper Drug design and repurposing with a sequence-to-drug paradigm

Chen, Lifan; Fan, Zisheng; Chang, Jie et al. · 2022 · DOI

Full title: Drug design and repurposing with a sequence-to-drug paradigm

Authors: Chen, Lifan; Fan, Zisheng; Chang, Jie; Yang, Ruirui; Guo, Hao; Zhang, Yinghui; Yang, Tianbiao; Zhou, Chenmao; Chen, Zhengyang; Chen, Zheng; Hao, Xinyue; Zhang, Keke; Cui, Rongrong; Ding, Yiluan; Zhang, Naixia; Luo, Xiaomin; Jiang, Hualiang; Zhang, Sulin; Zheng, Mingyue

Year: 2022

DOI: https://doi.org/10.1101/2022.03.26.485909

Paper Applying atomistic neural networks to bias conformer ensembles towards bioactive-like conformations

Baillif, Benoît; Cole, Jason C.; Giangreco, Ilenia et al. · 2023 · Journal of Cheminformatics · DOI

Full title: Applying atomistic neural networks to bias conformer ensembles towards bioactive-like conformations

Authors: Baillif, Benoît; Cole, Jason C.; Giangreco, Ilenia; McCabe, Patrick; Bender, Andreas

Year: 2023

Venue: Journal of Cheminformatics

DOI: https://doi.org/10.1186/s13321-023-00794-w

Paper Structural Insight into Geranylgeranyl Diphosphate Synthase (GGDPS) for Cancer Therapy

Pham, Andrew C.; Holstein, Sarah A.; Dasgupta, Medhanjali · 2023 · Molecular Cancer Therapeutics · DOI

Full title: Structural Insight into Geranylgeranyl Diphosphate Synthase (GGDPS) for Cancer Therapy

Authors: Pham, Andrew C.; Holstein, Sarah A.; Dasgupta, Medhanjali

Year: 2023

Venue: Molecular Cancer Therapeutics

DOI: https://doi.org/10.1158/1535-7163.mct-23-0358

Paper Deep contrastive learning enables genome-wide virtual screening.

Jia, Yinjun; Gao, Bowen; Tan, Jiaxin et al. · 2026 · Science (New York, N.Y.) · DOI

Full title: Deep contrastive learning enables genome-wide virtual screening.

Authors: Jia, Yinjun; Gao, Bowen; Tan, Jiaxin; Zheng, Jiqing; Hong, Xin; Zhu, Wenyu; Tan, Haichuan; Xiao, Yuan; Tan, Liping; Cai, Hongyi; Huang, Yanwen; Deng, Zhiheng; Wu, Xiangwei; Jin, Yue; Yuan, Yafei; Tian, Jiekang; He, Wei; Ma, Weiying; Zhang, Yaqin; Liu, Lei; Yan, Chuangye; Zhang, Wei; Lan, Yanyan

Year: 2026

Venue: Science (New York, N.Y.)

DOI: https://doi.org/10.1126/science.ads9530

Paper In silico studies of the open form of human tissue transglutaminase

Vlasov, A.V.; Ivashchenko, Sergey; Shulga, Dmitry A. et al. · 2024 · Research Square (Research Square) · DOI

Full title: In silico studies of the open form of human tissue transglutaminase

Authors: Vlasov, A.V.; Ivashchenko, Sergey; Shulga, Dmitry A.; Иващенко, В. А.; Zinovev, Egor V.

Year: 2024

Venue: Research Square (Research Square)

DOI: https://doi.org/10.21203/rs.3.rs-3937740/v1

Paper Prediction of protein–ligand binding affinity via deep learning models

Wang, Huiwen · 2024 · Briefings in Bioinformatics · DOI

Full title: Prediction of protein–ligand binding affinity via deep learning models

Authors: Wang, Huiwen

Year: 2024

Venue: Briefings in Bioinformatics

DOI: https://doi.org/10.1093/bib/bbae081

Paper In silico discovery of potent inhibitors against monkeypox’s major structural proteins

K. Lokhande; A. Shrivastava; Ashutosh Kumar Singh · 2023 · Journal of Biomolecular Structure and Dynamics · DOI

Full title: In silico discovery of potent inhibitors against monkeypox’s major structural proteins

Authors: K. Lokhande; A. Shrivastava; Ashutosh Kumar Singh

Year: 2023

Venue: Journal of Biomolecular Structure and Dynamics

DOI: https://doi.org/10.1080/07391102.2023.2183342

Paper FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction

Alex Morehead; Jianlin Cheng · 2024 · arXiv.org · DOI

Full title: FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction

Authors: Alex Morehead; Jianlin Cheng

Year: 2024

Venue: arXiv.org

DOI: https://doi.org/10.48550/arxiv.2412.10966

Paper TopoQA: a topological deep learning-based approach for protein complex structure interface quality assessment.

Han, Bingqing; Zhang, Yipeng; Li, Longlong et al. · 2025 · Briefings in bioinformatics · DOI

Full title: TopoQA: a topological deep learning-based approach for protein complex structure interface quality assessment.

Authors: Han, Bingqing; Zhang, Yipeng; Li, Longlong; Gong, Xinqi; Xia, Kelin

Year: 2025

Venue: Briefings in bioinformatics

DOI: https://doi.org/10.1093/bib/bbaf083

Paper Neural Networks to Calculate CDK2 Inhibition.

de Azevedo, Walter Filgueira · 2026 · Methods in molecular biology (Clifton, N.J.) · DOI

Full title: Neural Networks to Calculate CDK2 Inhibition.

Authors: de Azevedo, Walter Filgueira

Year: 2026

Venue: Methods in molecular biology (Clifton, N.J.)

DOI: https://doi.org/10.1007/978-1-0716-4949-7_19

Paper SAnDReS 2.0: Development of machine-learning models to explore the scoring function space.

de Azevedo, Walter Filgueira; Quiroga, Rodrigo; Villarreal, Marcos Ariel et al. · 2024 · Journal of computational chemistry · DOI

Full title: SAnDReS 2.0: Development of machine-learning models to explore the scoring function space.

Authors: de Azevedo, Walter Filgueira; Quiroga, Rodrigo; Villarreal, Marcos Ariel; da Silveira, Nelson José Freitas; Bitencourt-Ferreira, Gabriela; da Silva, Amauri Duarte; Veit-Acosta, Martina; Oliveira, Patricia Rufino; Tutone, Marco; Biziukova, Nadezhda; Poroikov, Vladimir; Tarasova, Olga; Baud, Stéphaine

Year: 2024

Venue: Journal of computational chemistry

DOI: https://doi.org/10.1002/jcc.27449

Paper Critical assessment of methods of protein structure prediction ( CASP )—Round XV

Kryshtafovych, Andriy; Schwede, Torsten; Topf, Maya et al. · 2023 · Proteins Structure Function and Bioinformatics · DOI

Full title: Critical assessment of methods of protein structure prediction ( CASP )—Round XV

Authors: Kryshtafovych, Andriy; Schwede, Torsten; Topf, Maya; Fidelis, Krzysztof; Moult, John

Year: 2023

Venue: Proteins Structure Function and Bioinformatics

DOI: https://doi.org/10.1002/prot.26617

Paper In silico screening of IMPPAT-derived phytochemicals targeting ERG6 and drug resistance–associated proteins in drug-resistant Candida albicans: virtual screening and molecular dynamics using alphafold models

Akshay Kisan Mundhe; Premanand Adaikalasamy; Reena Rajkumari Baskaran · 2026 · In Silico Pharmacology · DOI

Full title: In silico screening of IMPPAT-derived phytochemicals targeting ERG6 and drug resistance–associated proteins in drug-resistant Candida albicans: virtual screening and molecular dynamics using alphafold models

Authors: Akshay Kisan Mundhe; Premanand Adaikalasamy; Reena Rajkumari Baskaran

Year: 2026

Venue: In Silico Pharmacology

DOI: https://doi.org/10.1007/s40203-025-00480-9

Paper Quantum chemical optimization and residue-specific stabilization of CDK20 inhibitors in hepatocellular carcinoma.

Foudah, Ahmed I; Alqarni, Mohammed H; Aljarba, Tariq M et al. · 2025 · Molecular diversity · DOI

Full title: Quantum chemical optimization and residue-specific stabilization of CDK20 inhibitors in hepatocellular carcinoma.

Authors: Foudah, Ahmed I; Alqarni, Mohammed H; Aljarba, Tariq M; Jawaid, Talha; Alkhamees, Osama A; Alsanad, Saud M; AlHussaini, Khalid I; Alam, Aftab

Year: 2025

Venue: Molecular diversity

DOI: https://doi.org/10.1007/s11030-025-11339-8

Paper Binding mode of brazzein to the taste receptor based on crystal structure and docking simulation.

Kim, Tae-Yeon; Woo, Eui-Jeon; Yoon, Tae-Sung · 2022 · Biochemical and biophysical research communications · DOI

Full title: Binding mode of brazzein to the taste receptor based on crystal structure and docking simulation.

Authors: Kim, Tae-Yeon; Woo, Eui-Jeon; Yoon, Tae-Sung

Year: 2022

Venue: Biochemical and biophysical research communications

DOI: https://doi.org/10.1016/j.bbrc.2022.01.004

Paper An Integrated Computational and Biophysical Approach for Investigating the Structure-Function Impact of blaOXA-58 Mutations in Acinetobacter baumannii.

Jalil, Huma; Jalil, Hina; Mir, Shazia Shaheen et al. · 2026 · Molecular biotechnology · DOI

Full title: An Integrated Computational and Biophysical Approach for Investigating the Structure-Function Impact of blaOXA-58 Mutations in Acinetobacter baumannii.

Authors: Jalil, Huma; Jalil, Hina; Mir, Shazia Shaheen; Amin, Saad; Khan, Kalsoom; Ullah, Asad; Khan, Ibrar; Azam, Sadiq; Ahmad, Sajjad

Year: 2026

Venue: Molecular biotechnology

DOI: https://doi.org/10.1007/s12033-026-01553-6

Paper Structure of epoxide hydrolase 2 from Mangifera indica throws light on the substrate specificity determinants of plant epoxide hydrolases.

Bhoite, Ashwini; Gaur, Neeraj K; Palange, Megha et al. · 2024 · Biochemical and biophysical research communications · DOI

Full title: Structure of epoxide hydrolase 2 from Mangifera indica throws light on the substrate specificity determinants of plant epoxide hydrolases.

Authors: Bhoite, Ashwini; Gaur, Neeraj K; Palange, Megha; Kontham, Ravindar; Gupta, Vidya; Kulkarni, Kiran

Year: 2024

Venue: Biochemical and biophysical research communications

DOI: https://doi.org/10.1016/j.bbrc.2024.150444

Paper Structure-based identification of small molecule inhibitors targeting trigger factor and peptidyl prolyl cis/trans isomerase B (PpiB) of Bacillus anthracis Sterne: Towards new therapeutic interventions against anthrax.

Roopshali Rakshit; Aayush Bahl; G. Gautam et al. · 2025 · Journal of Molecular Graphics and Modelling · DOI

Full title: Structure-based identification of small molecule inhibitors targeting trigger factor and peptidyl prolyl cis/trans isomerase B (PpiB) of Bacillus anthracis Sterne: Towards new therapeutic interventions against anthrax.

Authors: Roopshali Rakshit; Aayush Bahl; G. Gautam; Saurabh Pandey; Deeksha Tripathi

Year: 2025

Venue: Journal of Molecular Graphics and Modelling

DOI: https://doi.org/10.1016/j.jmgm.2025.109185

Paper An automated pipeline integrating AlphaFold 2 and MODELLER for protein structure prediction

Zuluaga, Fabio Hernán Gil; D’Arminio, Nancy; Bardozzo, Francesco et al. · 2023 · Computational and Structural Biotechnology Journal · DOI

Full title: An automated pipeline integrating AlphaFold 2 and MODELLER for protein structure prediction

Authors: Zuluaga, Fabio Hernán Gil; D’Arminio, Nancy; Bardozzo, Francesco; Tagliaferri, Roberto; Marabotti, Anna

Year: 2023

Venue: Computational and Structural Biotechnology Journal

DOI: https://doi.org/10.1016/j.csbj.2023.10.056

Paper Computational modeling and prediction of deletion mutants.

Woods, Hope; Schiano, Dominic L; Aguirre, Jonathan I et al. · 2023 · Structure (London, England : 1993) · DOI

Full title: Computational modeling and prediction of deletion mutants.

Authors: Woods, Hope; Schiano, Dominic L; Aguirre, Jonathan I; Ledwitch, Kaitlyn V; McDonald, Eli F; Voehler, Markus; Meiler, Jens; Schoeder, Clara T

Year: 2023

Venue: Structure (London, England : 1993)

DOI: https://doi.org/10.1016/j.str.2023.04.005

Paper In-Silico targeting of SARS-CoV-2 NSP6 for drug and natural products repurposing.

Abdelkader, Ahmed; Elzemrany, Amal A; El-Nadi, Mennatullah et al. · 2022 · Virology · DOI

Full title: In-Silico targeting of SARS-CoV-2 NSP6 for drug and natural products repurposing.

Authors: Abdelkader, Ahmed; Elzemrany, Amal A; El-Nadi, Mennatullah; Elsabbagh, Sherif A; Shehata, Moustafa A; Eldehna, Wagdy M; El-Hadidi, Mohamed; Ibrahim, Tamer M

Year: 2022

Venue: Virology

DOI: https://doi.org/10.1016/j.virol.2022.06.008

Paper Benchmarking Refined and Unrefined AlphaFold2 Structures for Hit Discovery

Yuqi Zhang; Márton Vass; Da Shi et al. · 2023 · Journal of Chemical Information and Modeling · DOI

Full title: Benchmarking Refined and Unrefined AlphaFold2 Structures for Hit Discovery

Year: 2023

Venue: Journal of Chemical Information and Modeling

DOI: https://doi.org/10.1021/acs.jcim.2c01219

Paper Combining AlphaFold with Focused Virtual Library Design in the Development of Novel CCR2 and CCR5 Antagonists.

Essa, Khaled; Noorman van der Dussen, Kian; Yao, Yao et al. · 2025 · Journal of chemical information and modeling · DOI

Full title: Combining AlphaFold with Focused Virtual Library Design in the Development of Novel CCR2 and CCR5 Antagonists.

Authors: Essa, Khaled; Noorman van der Dussen, Kian; Yao, Yao; Bleijs, Bente; Ortiz Zacarias, Natalia V; Heitman, Laura H; van Westen, Gerard J P; Jespers, Willem; van der Es, Daan; Šícho, Martin

Year: 2025

Venue: Journal of chemical information and modeling

DOI: https://doi.org/10.1021/acs.jcim.5c01596

Paper Assessing AlphaFold 3 for Per- and Polyfluoroalkyl Substances Docking in Protein Structures

Gong, Xiping; Zhou, Hualu; Huang, Qingguo · 2025 · Environmental Science & Technology · DOI

Full title: Assessing AlphaFold 3 for Per- and Polyfluoroalkyl Substances Docking in Protein Structures

Authors: Gong, Xiping; Zhou, Hualu; Huang, Qingguo

Year: 2025

Venue: Environmental Science & Technology

DOI: https://doi.org/10.1021/acs.est.5c03917

Paper Integrating Machine Learning into Free Energy Perturbation Workflows

Donald J. M. van Pinxteren; Willem Jespers · 2025 · Journal of Chemical Information and Modeling · DOI

Full title: Integrating Machine Learning into Free Energy Perturbation Workflows

Authors: Donald J. M. van Pinxteren; Willem Jespers

Year: 2025

Venue: Journal of Chemical Information and Modeling

DOI: https://doi.org/10.1021/acs.jcim.5c01449

Paper AlphaFold2 versus experimental structures: evaluation on G protein-coupled receptors

He, Xinheng; You, Chongzhao; Jiang, Hualiang et al. · 2022 · Acta Pharmacologica Sinica · DOI

Full title: AlphaFold2 versus experimental structures: evaluation on G protein-coupled receptors

Authors: He, Xinheng; You, Chongzhao; Jiang, Hualiang; Jiang, Yi; Xu, H. Eric; Cheng, Xi

Year: 2022

Venue: Acta Pharmacologica Sinica

DOI: https://doi.org/10.1038/s41401-022-00938-y

Paper In-silico design of Multi-Epitope Vaccine Against Glioblastoma Using Tumor-Associated Antigens and TLR Agonist Adjuvants

Jamil, Muhammad · 2025 · DOI

Full title: In-silico design of Multi-Epitope Vaccine Against Glioblastoma Using Tumor-Associated Antigens and TLR Agonist Adjuvants

Authors: Jamil, Muhammad

Year: 2025

DOI: https://doi.org/10.21203/rs.3.rs-7225965/v1

Paper New computational methods to study the relationship between protein structure and function

Kumar, Ambuj · 2022 · DOI

Full title: New computational methods to study the relationship between protein structure and function

Authors: Kumar, Ambuj

Year: 2022

DOI: https://doi.org/10.31274/td-20240329-537

Paper In-silico analysis of papain fibrinolytic mechanism from Carica papaya

Purnomo, Jonathan Suciono; Dikson; SOENTORO, SAMUEL EMMANUEL et al. · 2025 · Asia-Pacific Journal of Molecular Biology and Biotechnology · DOI

Full title: In-silico analysis of papain fibrinolytic mechanism from Carica papaya

Authors: Purnomo, Jonathan Suciono; Dikson; SOENTORO, SAMUEL EMMANUEL; Erika; Sugata, Marcelia; Samantha, Ariela; Pinontoan, Reinhard

Year: 2025

Venue: Asia-Pacific Journal of Molecular Biology and Biotechnology

DOI: https://doi.org/10.35118/apjmbb.2025.033.2.17

Paper Modeling study of the HlyBD-TolC hemolysin secretion system using the AI-based structural prediction and molecular dynamics simulation

Baek, Yeongjin; Lee, Jinwook; Lee, Dukwon et al. · 2023 · Korean Society for Structural Biology · DOI

Full title: Modeling study of the HlyBD-TolC hemolysin secretion system using the AI-based structural prediction and molecular dynamics simulation

Authors: Baek, Yeongjin; Lee, Jinwook; Lee, Dukwon; Xu, Yongbin; Ha, Nam‐Chul

Year: 2023

Venue: Korean Society for Structural Biology

DOI: https://doi.org/10.34184/kssb.2023.11.2.21

Paper Applications of reinforcement learning, machine learning, and virtual screening in SARS-CoV-2-related proteins

Y. Matsuzaka; R. Yashiro · 2024 · Computing and Artificial Intelligence · DOI

Full title: Applications of reinforcement learning, machine learning, and virtual screening in SARS-CoV-2-related proteins

Authors: Y. Matsuzaka; R. Yashiro

Year: 2024

Venue: Computing and Artificial Intelligence

DOI: https://doi.org/10.59400/cai.v2i2.1279

Paper Atomistic simulations identify the Tetrandrine as potent anti-malarial drug candidate against Plasmodium falciparum targeting Heme Detoxification Protein (HDP).

Bux, Khair; Abbasi, Urooj; Hasan, Khwaja Ali et al. · 2026 · Journal of molecular graphics & modelling · DOI

Full title: Atomistic simulations identify the Tetrandrine as potent anti-malarial drug candidate against Plasmodium falciparum targeting Heme Detoxification Protein (HDP).

Authors: Bux, Khair; Abbasi, Urooj; Hasan, Khwaja Ali; Hussain, Armeen; Malik, Fateen; Herwig, Ralf

Year: 2026

Venue: Journal of molecular graphics & modelling

DOI: https://doi.org/10.1016/j.jmgm.2026.109311

Paper AlphaFold accelerated discovery of psychotropic agonists targeting the trace amine-associated receptor 1.

Díaz-Holguín, Alejandro; Saarinen, Marcus; Vo, Duc Duy et al. · 2024 · Science advances · DOI

Full title: AlphaFold accelerated discovery of psychotropic agonists targeting the trace amine-associated receptor 1.

Authors: Díaz-Holguín, Alejandro; Saarinen, Marcus; Vo, Duc Duy; Sturchio, Andrea; Branzell, Niclas; Cabeza de Vaca, Israel; Hu, Huabin; Mitjavila-Domènech, Núria; Lindqvist, Annika; Baranczewski, Pawel; Millan, Mark J; Yang, Yunting; Carlsson, Jens; Svenningsson, Per

Year: 2024

Venue: Science advances

DOI: https://doi.org/10.1126/sciadv.adn1524

Thesis Computational studies of folding and binding of polypeptides

Turpin, Eleanor R. · 2013 · University of Nottingham · DOI

Full title: Computational studies of folding and binding of polypeptides

Authors: Turpin, Eleanor R.

Year: 2013

Venue: University of Nottingham

DOI: https://eprints.nottingham.ac.uk/13644/1/FINAL_thesis_corrections_ETurpin.pdf

Thesis Computational approaches for multi-OMICs data analysis towards rational drug design

Koohi-Moghadam, Mohamad · 2019 · University of Hong Kong · DOI

Full title: Computational approaches for multi-OMICs data analysis towards rational drug design

Authors: Koohi-Moghadam, Mohamad

Year: 2019

Venue: University of Hong Kong

DOI: https://hub.hku.hk/handle/10722/273758

Thesis Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold

Day, Austin L.; Greisen, Per; Doyle, Lindsey et al. · 2019 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold

Authors: Day, Austin L.; Greisen, Per; Doyle, Lindsey; Schena, Alberto; Stella, Nephi; Johnsson, Kai; Baker, David; Stoddard, Barry

Year: 2019

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/162299

Thesis Critical assessment of approaches for molecular docking to elucidate associations of HLA alleles with adverse drug reactions.

Ramsbottom, Kerry A; Carr, Daniel F; Jones, Andrew R et al. · 2018 · University of Liverpool · DOI

Full title: Critical assessment of approaches for molecular docking to elucidate associations of HLA alleles with adverse drug reactions.

Authors: Ramsbottom, Kerry A; Carr, Daniel F; Jones, Andrew R; Rigden, Daniel J

Year: 2018

Venue: University of Liverpool

DOI: https://livrepository.liverpool.ac.uk/3025004/1/Ramsbottom_et_al_revised_marked.docx

Thesis A base measure of precision for protein stability predictors: structural sensitivity

Caldararu, Octav; Blundell, Tom L; Kepp, Kasper Planeta et al. · 2021 · Technical University of Denmark (DTU) · DOI

Full title: A base measure of precision for protein stability predictors: structural sensitivity

Authors: Caldararu, Octav; Blundell, Tom L; Kepp, Kasper Planeta; id_orcid 0000-0002-6754-7348

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/991a8d71-b422-4028-9799-26e55e43417a

Thesis In silico identification of noncompetitive inhibitors targeting an uncharacterized allosteric site of falcipain-2

Hernández González, Jorge Enrique [UNESP]; Salas-Sarduy, Emir; Hernández Alvarez, Lilian [UNESP] et al. · 2022 · Universidade Estadual Paulista (UNESP) · DOI

Full title: In silico identification of noncompetitive inhibitors targeting an uncharacterized allosteric site of falcipain-2

Authors: Hernández González, Jorge Enrique [UNESP]; Salas-Sarduy, Emir; Hernández Alvarez, Lilian [UNESP]; Barreto Gomes, Diego Enry; Pascutti, Pedro Geraldo; Oostenbrink, Chris; Leite, Vitor B. P. [UNESP]

Year: 2022

Venue: Universidade Estadual Paulista (UNESP)

DOI: http://dx.doi.org/10.1007/s10822-021-00420-7

Thesis Correcting the impact of docking pose generation error on binding affinity prediction

Ballester, Pedro; Li, H; Leung, K et al. · 2024 · Imperial College London · DOI

Full title: Correcting the impact of docking pose generation error on binding affinity prediction

Authors: Ballester, Pedro; Li, H; Leung, K; Wong, M; Ballester, PJ

Year: 2024

Venue: Imperial College London

DOI: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1169-4

Thesis Implications of AlphaFold2 for crystallographic phasing by molecular replacement.

McCoy, Airlie J; Sammito, Massimo D; Read, Randy J · 2022 · University of Cambridge · DOI

Full title: Implications of AlphaFold2 for crystallographic phasing by molecular replacement.

Authors: McCoy, Airlie J; Sammito, Massimo D; Read, Randy J

Year: 2022

Venue: University of Cambridge

DOI: https://www.repository.cam.ac.uk/handle/1810/333679

Thesis Accelerating crystal structure determination with iterative AlphaFold prediction.

Terwilliger, Thomas C; Afonine, Pavel V; Liebschner, Dorothee et al. · 2023 · University of Cambridge · DOI

Full title: Accelerating crystal structure determination with iterative AlphaFold prediction.

Authors: Terwilliger, Thomas C; Afonine, Pavel V; Liebschner, Dorothee; Croll, Tristan I; McCoy, Airlie J; Oeffner, Robert D; Williams, Christopher J; Poon, Billy K; Richardson, Jane S; Read, Randy J; Adams, Paul D

Year: 2023

Venue: University of Cambridge

DOI: https://www.repository.cam.ac.uk/handle/1810/346944

Thesis A new protocol to improve the predictive power of molecular docking

Basciu, A.; Pietrucci, F.; Bonvin, A.M.J.J. et al. · 2017 · Utrecht University · DOI

Full title: A new protocol to improve the predictive power of molecular docking

Authors: Basciu, A.; Pietrucci, F.; Bonvin, A.M.J.J.; Vargiu, A.V.

Year: 2017

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/361093

Thesis Towards the accurate modelling of antibody-antigen complexes from sequence using machine learning and information-driven docking

Giulini, Marco; Schneider, Constantin; Cutting, Daniel et al. · 2023 · Utrecht University · DOI

Full title: Towards the accurate modelling of antibody-antigen complexes from sequence using machine learning and information-driven docking

Authors: Giulini, Marco; Schneider, Constantin; Cutting, Daniel; Desai, Nikita; Deane, Charlotte M.; Bonvin, Alexandre M.J.J.

Year: 2023

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/436001

Thesis DeepRank-GNN-esm: A Graph Neural Network for Scoring Protein-Protein Models using Protein Language Model

Xu, X.; Bonvin, A. M. J. J. · 2023 · Utrecht University · DOI

Full title: DeepRank-GNN-esm: A Graph Neural Network for Scoring Protein-Protein Models using Protein Language Model

Authors: Xu, X.; Bonvin, A. M. J. J.

Year: 2023

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/436014

Thesis Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment

Lensink, Marc F; Brysbaert, Guillaume; Raouraoua, Nessim et al. · 2023 · Utrecht University · DOI

Full title: Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment

Authors: Lensink, Marc F; Brysbaert, Guillaume; Raouraoua, Nessim; Bates, Paul A; Giulini, Marco; Honorato, Rodrigo V; van Noort, Charlotte; Teixeira, Joao M C; Bonvin, Alexandre M J J; Kong, Ren; Shi, Hang; Lu, Xufeng; Chang, Shan; Liu, Jian; Guo, Zhiye; Chen, Xiao; Morehead, Alex; Roy, Raj S; Wu, Tianqi; Giri, Nabin; Quadir, Farhan; Chen, Chen; Cheng, Jianlin; Del Carpio, Carlos A; Ichiishi, Eichiro; Rodriguez-Lumbreras, Luis A; Fernandez-Recio, Juan; Harmalkar, Ameya; Chu, Lee-Shin; Canner, Sam; Smanta, Rituparna; Gray, Jeffrey J; Li, Hao; Lin, Peicong; He, Jiahua; Tao, Huanyu; Huang, Sheng-You; Roel-Touris, Jorge; Jimenez-Garcia, Brian; Christoffer, Charles W; Jain, Anika J; Kagaya, Yuki; Kannan, Harini; Nakamura, Tsukasa; Terashi, Genki; Verburgt, Jacob C; Zhang, Yuanyuan; Zhang, Zicong; Fujuta, Hayato; Sekijima, Masakazu; Kihara, Daisuke; Khan, Omeir; Kotelnikov, Sergei; Ghani, Usman; Padhorny, Dzmitry; Beglov, Dmitri; Vajda, Sandor; Kozakov, Dima; Negi, Surendra S; Ricciardelli, Tiziana; Barradas-Bautista, Didier; Cao, Zhen; Chawla, Mohit; Cavallo, Luigi; Oliva, Romina; Yin, Rujie; Cheung, Melyssa; Guest, Johnathan D; Lee, Jessica; Pierce, Brian G; Shor, Ben; Cohen, Tomer; Halfon, Matan; Schneidman-Duhovny, Dina; Zhu, Shaowen; Yin, Rujie; Sun, Yuanfei; Shen, Yang; Maszota-Zieleniak, Martyna; Bojarski, Krzysztof K; Lubecka, Emilia A; Marcisz, Mateusz; Danielsson, Annemarie; Dziadek, Lukasz; Gaardlos, Margrethe; Gieldon, Artur; Liwo, Adam; Samsonov, Sergey A; Slusarz, Rafal; Zieba, Karolina; Sieradzan, Adam K; Czaplewski, Cezary; Kobayashi, Shinpei; Miyakawa, Yuta; Kiyota, Yasuomi; Takeda-Shitaka, Mayuko; Olechnovic, Kliment; Valancauskas, Lukas; Dapkunas, Justas; Venclovas, Ceslovas; Wallner, Bjorn; Yang, Lin; Hou, Chengyu; He, Xiaodong; Guo, Shuai; Jiang, Shenda; Ma, Xiaoliang; Duan, Rui; Qui, Liming; Xu, Xianjin; Zou, Xiaoqin; Velankar, Sameer; Wodak, Shoshana J

Year: 2023

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/434472

Thesis Towards a structurally resolved human protein interaction network

Burke, David F; Bryant, Patrick; Barrio-Hernandez, Inigo et al. · 2023 · Utrecht University · DOI

Full title: Towards a structurally resolved human protein interaction network

Authors: Burke, David F; Bryant, Patrick; Barrio-Hernandez, Inigo; Memon, Danish; Pozzati, Gabriele; Shenoy, Aditi; Zhu, Wensi; Dunham, Alistair S; Albanese, Pascal; Keller, Andrew; Scheltema, Richard A; Bruce, James E; Leitner, Alexander; Kundrotas, Petras; Beltrao, Pedro; Elofsson, Arne

Year: 2023

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/434734

Thesis Factor XII Explored with AlphaFold - Opportunities for Selective Drug Development

Frunt, Rowan; El Otmani, Hinde; Gibril Kaira, Bubacarr et al. · 2023 · Utrecht University · DOI

Full title: Factor XII Explored with AlphaFold - Opportunities for Selective Drug Development

Authors: Frunt, Rowan; El Otmani, Hinde; Gibril Kaira, Bubacarr; de Maat, Steven; Maas, Coen

Year: 2023

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/448024

Thesis DeepRank-GNN-esm: A graph neural network for scoring protein-protein models using protein language model

Xu, Xiaotong; Bonvin, Alexandre M.J.J. · 2024 · Utrecht University · DOI

Full title: DeepRank-GNN-esm: A graph neural network for scoring protein-protein models using protein language model

Authors: Xu, Xiaotong; Bonvin, Alexandre M.J.J.

Year: 2024

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/438082

Thesis Benchmarking AlphaFold ‐enabled molecular docking predictions for antibiotic discovery

Wong, Felix; Krishnan, Aarti; Zheng, Erica J et al. · 2023 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Benchmarking AlphaFold ‐enabled molecular docking predictions for antibiotic discovery

Authors: Wong, Felix; Krishnan, Aarti; Zheng, Erica J; Stärk, Hannes; Manson, Abigail L; Earl, Ashlee M; Jaakkola, Tommi; Collins, James J

Year: 2023

Venue: Massachusetts Institute of Technology (MIT)

DOI: https://hdl.handle.net/1721.1/147788

Thesis Deep learning for low-data drug discovery: Hurdles and opportunities

van Tilborg, Derek; Brinkmann, Helena; Criscuolo, Emanuele et al. · 2024 · Utrecht University · DOI

Full title: Deep learning for low-data drug discovery: Hurdles and opportunities

Authors: van Tilborg, Derek; Brinkmann, Helena; Criscuolo, Emanuele; Rossen, Luke; Özçelik, Rıza; Grisoni, Francesca

Year: 2024

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/456135

Thesis Pareto Optimization to Accelerate Multi-Objective Virtual Screening

Fromer, Jenna C.; Graff, David E.; Coley, Connor W. · 2024 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Pareto Optimization to Accelerate Multi-Objective Virtual Screening

Authors: Fromer, Jenna C.; Graff, David E.; Coley, Connor W.

Year: 2024

Venue: Massachusetts Institute of Technology (MIT)

DOI: https://hdl.handle.net/1721.1/156714

Thesis DeepRank-GNN-esm: A graph neural network for scoring protein-protein models using protein language model

Xu, Xiaotong; Bonvin, Alexandre M.J.J. · 2024 · Utrecht University · DOI

Full title: DeepRank-GNN-esm: A graph neural network for scoring protein-protein models using protein language model

Authors: Xu, Xiaotong; Bonvin, Alexandre M.J.J.

Year: 2024

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/437608

Thesis Continuous Automated Model Evaluation (CAMEO)-Perspectives on the future of fully automated evaluation of structure prediction methods

Robin, Xavier; Haas, Juergen; Gumienny, Rafal et al. · 2025 · University of Basel - edoc Repository · DOI

Full title: Continuous Automated Model Evaluation (CAMEO)-Perspectives on the future of fully automated evaluation of structure prediction methods

Authors: Robin, Xavier; Haas, Juergen; Gumienny, Rafal; Smolinski, Anna; Tauriello, Gerardo; Schwede, Torsten

Year: 2025

Venue: University of Basel - edoc Repository

DOI: http://hdl.handle.net/20.500.14716/118292

Thesis A structural biology community assessment of AlphaFold2 applications

Akdel, Mehmet; Pires, Douglas E. V.; Pardo, Eduard Porta et al. · 2025 · University of Basel - edoc Repository · DOI

Full title: A structural biology community assessment of AlphaFold2 applications

Authors: Akdel, Mehmet; Pires, Douglas E. V.; Pardo, Eduard Porta; Jänes, Jürgen; Zalevsky, Arthur O.; Mészáros, Bálint; Bryant, Patrick; Good, Lydia L.; Laskowski, Roman A.; Pozzati, Gabriele; Shenoy, Aditi; Zhu, Wensi; Kundrotas, Petras; Serra, Victoria Ruiz; Rodrigues, Carlos H. M.; Dunham, Alistair S.; Burke, David; Borkakoti, Neera; Velankar, Sameer; Frost, Adam; Basquin, Jérôme; Lindorff-Larsen, Kresten; Bateman, Alex; Kajava, Andrey V.; Valencia, Alfonso; Ovchinnikov, Sergey; Durairaj, Janani; Ascher, David B.; Thornton, Janet M.; Davey, Norman E.; Stein, Amelie; Elofsson, Arne; Croll, Tristan I.; Beltrao, Pedro

Year: 2025

Venue: University of Basel - edoc Repository

DOI: http://hdl.handle.net/20.500.14716/121153

Thesis Modelling three-dimensional protein structures for applications in drug design

Schmidt, Tobias; Bergner, Andreas; Schwede, Torsten · 2025 · University of Basel - edoc Repository · DOI

Full title: Modelling three-dimensional protein structures for applications in drug design

Authors: Schmidt, Tobias; Bergner, Andreas; Schwede, Torsten

Year: 2025

Venue: University of Basel - edoc Repository

DOI: http://hdl.handle.net/20.500.14716/90374

Thesis Critical assessment of methods of protein structure prediction (CASP) - Round XII

Moult, John; Fidelis, Krzysztof; Kryshtafovych, Andriy et al. · 2025 · University of Basel - edoc Repository · DOI

Full title: Critical assessment of methods of protein structure prediction (CASP) - Round XII

Authors: Moult, John; Fidelis, Krzysztof; Kryshtafovych, Andriy; Schwede, Torsten; Tramontano, Anna

Year: 2025

Venue: University of Basel - edoc Repository

DOI: http://hdl.handle.net/20.500.14716/104201

Thesis Protein modeling: what happened to the "protein structure gap"?

Schwede, Torsten · 2025 · University of Basel - edoc Repository · DOI

Full title: Protein modeling: what happened to the "protein structure gap"?

Authors: Schwede, Torsten

Year: 2025

Venue: University of Basel - edoc Repository

DOI: http://hdl.handle.net/20.500.14716/89666

Thesis Elucidating the multiple roles of hydration for accurate protein-ligand binding prediction via deep learning

Mahmoud, Amr H.; Masters, Matthew R.; Yang, Ying et al. · 2025 · University of Basel - edoc Repository · DOI

Full title: Elucidating the multiple roles of hydration for accurate protein-ligand binding prediction via deep learning

Authors: Mahmoud, Amr H.; Masters, Matthew R.; Yang, Ying; Lill, Markus A.

Year: 2025

Venue: University of Basel - edoc Repository

DOI: http://hdl.handle.net/20.500.14716/116200

Thesis Molecular simulation of protein-ligand complexes

Guest, Ellen · 2022 · University of Nottingham · DOI

Full title: Molecular simulation of protein-ligand complexes

Authors: Guest, Ellen

Year: 2022

Venue: University of Nottingham

DOI: https://eprints.nottingham.ac.uk/68947/1/thesis_corrected.pdf

Thesis Structural exploration of cannabinoid receptors using computational methods

Murali, Lahari · 2020 · University of Nottingham · DOI

Full title: Structural exploration of cannabinoid receptors using computational methods

Authors: Murali, Lahari

Year: 2020

Venue: University of Nottingham

DOI: https://eprints.nottingham.ac.uk/60398/1/Thesis-CorrectedCopy-LM-15042020.pdf

Thesis Biophysical studies of protein-ligand interactions and the discovery of FKBP12 inhibitors

Blackburn, Elizabeth Anne · 2012 · The University of Edinburgh · DOI

Full title: Biophysical studies of protein-ligand interactions and the discovery of FKBP12 inhibitors

Authors: Blackburn, Elizabeth Anne

Year: 2012

Venue: The University of Edinburgh

DOI: http://hdl.handle.net/1842/6504

Thesis Study of the N-terminal domains of MDM2 and MDM4, and their potential for targeting by small-molecule drugs

Sanchez Perez, Maria Concepcion · 2014 · The University of Edinburgh · DOI

Full title: Study of the N-terminal domains of MDM2 and MDM4, and their potential for targeting by small-molecule drugs

Authors: Sanchez Perez, Maria Concepcion

Year: 2014

Venue: The University of Edinburgh

DOI: http://hdl.handle.net/1842/8763

Thesis Integrating Emerging Computational Methods to More Reliably Identify and Optimize Antibodies with Functional Activity

Anderson, Kyle James · 2025 · University of California, San Francisco (UCSF) · DOI

Full title: Integrating Emerging Computational Methods to More Reliably Identify and Optimize Antibodies with Functional Activity

Authors: Anderson, Kyle James

Year: 2025

Venue: University of California, San Francisco (UCSF)

DOI: https://escholarship.org/uc/item/46h5w7df

Thesis De Novo Protein Design and Small Molecule Docking of Voltage-Gated Ion Channel Modulators Using Rosetta Methods

Harris, Brandon John · 2024 · University of California, Davis · DOI

Full title: De Novo Protein Design and Small Molecule Docking of Voltage-Gated Ion Channel Modulators Using Rosetta Methods

Authors: Harris, Brandon John

Year: 2024

Venue: University of California, Davis

DOI: https://escholarship.org/uc/item/7m86g04w

Thesis Identifying Potent Compounds Using Pairwise Consensus Methods

Xu, Marc; Wu, Chenyang; Wang, Shiyu et al. · 2025 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Identifying Potent Compounds Using Pairwise Consensus Methods

Authors: Xu, Marc; Wu, Chenyang; Wang, Shiyu; Zhan, Wenjin; Guo, Liwei; Li, Yi; Vogel, Horst; Yuan, Shuguang

Year: 2025

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/250223

Thesis Practical outcomes from CASP16 for users in need of biomolecular structure prediction

Abriata, Luciano A.; Dal Peraro, Matteo · 2025 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Practical outcomes from CASP16 for users in need of biomolecular structure prediction

Authors: Abriata, Luciano A.; Dal Peraro, Matteo

Year: 2025

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/251800

Thesis Decoding surface fingerprints for protein-ligand interactions

Ferreira De Sousa Correia, Bruno Emanuel; Bronstein, Michael; Igashov, Llia · 2025 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Decoding surface fingerprints for protein-ligand interactions

Authors: Ferreira De Sousa Correia, Bruno Emanuel; Bronstein, Michael; Igashov, Llia

Year: 2025

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/246398

Thesis Assessing and enhancing foldability in designed proteins

Listov, Dina; Lipsh-Sokolik, Rosalie; Rosset, Stephane et al. · 2022 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Assessing and enhancing foldability in designed proteins

Authors: Listov, Dina; Lipsh-Sokolik, Rosalie; Rosset, Stephane; Yang, Che; Correia, Bruno E.; Fleishman, Sarel Jacob

Year: 2022

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/190312

Thesis State-of-the-art web services for de novo protein structure prediction

Abriata, Luciano A.; Dal Peraro, Matteo · 2021 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: State-of-the-art web services for de novo protein structure prediction

Authors: Abriata, Luciano A.; Dal Peraro, Matteo

Year: 2021

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/182842

Thesis Improvements in Molecular Mechanics Sampling and Energy Models

Bylund, Joseph · 2014 · Columbia University · DOI

Full title: Improvements in Molecular Mechanics Sampling and Energy Models

Authors: Bylund, Joseph

Year: 2014

Venue: Columbia University

DOI: https://doi.org/10.7916/D80G3H7B

Thesis Advances in structure and small molecule docking predictions for crystallized G-Protein coupled receptors

Goldfeld, Dahlia A. · 2013 · Columbia University · DOI

Full title: Advances in structure and small molecule docking predictions for crystallized G-Protein coupled receptors

Authors: Goldfeld, Dahlia A.

Year: 2013

Venue: Columbia University

DOI: https://doi.org/10.7916/D8348SRR

Thesis Investigating protein flexibility using molecular dynamics simulations of α-1 acid glycoprotein and large-scale normal mode analysis of AlphaFold models

Dixit, Bhawna · 2025 · Ghent University (Universiteit Gent) · DOI

Full title: Investigating protein flexibility using molecular dynamics simulations of α-1 acid glycoprotein and large-scale normal mode analysis of AlphaFold models

Authors: Dixit, Bhawna

Year: 2025

Venue: Ghent University (Universiteit Gent)

DOI: https://biblio.ugent.be/publication/01JNK40KCK0R81GQ5P86KTSFNC

Thesis Multiscale Structural and Biophysical Studies of Protein-Compound Interactions

Trudeau, Stephen Joseph · 2024 · Columbia University · DOI

Full title: Multiscale Structural and Biophysical Studies of Protein-Compound Interactions

Authors: Trudeau, Stephen Joseph

Year: 2024

Venue: Columbia University

DOI: https://doi.org/10.7916/gnd3-mf07

Thesis Computational approaches for identifying bioactive compounds inhibiting SARS-CoV-2 main protease

Pojtanadithee, Piyatida · 2022 · Chulalongkorn University · DOI

Full title: Computational approaches for identifying bioactive compounds inhibiting SARS-CoV-2 main protease

Authors: Pojtanadithee, Piyatida

Year: 2022

Venue: Chulalongkorn University

DOI: https://digital.car.chula.ac.th/chulaetd/5732

Thesis Computational Modeling of Macrocycles and Structure-Based Design of Novel Antibacterial Compounds

Olanders, Gustav · 2021 · Uppsala University · DOI

Full title: Computational Modeling of Macrocycles and Structure-Based Design of Novel Antibacterial Compounds

Authors: Olanders, Gustav

Year: 2021

Venue: Uppsala University

DOI: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-445956

Thesis Molecular simulations of G protein-coupled receptors : A journey into structure-based ligand design and receptor function

Matricon, Pierre · 2021 · Uppsala University · DOI

Full title: Molecular simulations of G protein-coupled receptors : A journey into structure-based ligand design and receptor function

Authors: Matricon, Pierre

Year: 2021

Venue: Uppsala University

DOI: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-434103

Thesis Free energy calculations of G protein-coupled receptor modulation : New methods and applications

Jespers, Willem · 2020 · Uppsala University · DOI

Full title: Free energy calculations of G protein-coupled receptor modulation : New methods and applications

Authors: Jespers, Willem

Year: 2020

Venue: Uppsala University

DOI: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-407840

Thesis Structure-based Virtual Screening for Ligands of G Protein-coupled Receptors : Design of Allosteric and Dual-Target Modulators

Kampen, Stefanie · 2022 · Uppsala University · DOI

Full title: Structure-based Virtual Screening for Ligands of G Protein-coupled Receptors : Design of Allosteric and Dual-Target Modulators

Authors: Kampen, Stefanie

Year: 2022

Venue: Uppsala University

DOI: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-472101

Thesis New Paradigms in GPCR Drug Discovery : Structure Prediction and Design of Ligands with Tailored Properties

Jaiteh, Mariama · 2020 · Uppsala University · DOI

Full title: New Paradigms in GPCR Drug Discovery : Structure Prediction and Design of Ligands with Tailored Properties

Authors: Jaiteh, Mariama

Year: 2020

Venue: Uppsala University

DOI: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-399133

Thesis Discovery of Chemical Probes through Structure-based Virtual Screening of Vast Compound Databases

Luttens, Andreas · 2023 · Uppsala University · DOI

Full title: Discovery of Chemical Probes through Structure-based Virtual Screening of Vast Compound Databases

Authors: Luttens, Andreas

Year: 2023

Venue: Uppsala University

DOI: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-500083

Thesis A further leap of improvement in tertiary structure prediction in CASP13 prompts new routes for future assessments

Abriata, Luciano A.; Tamo, Giorgio E.; Dal Peraro, Matteo · 2019 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: A further leap of improvement in tertiary structure prediction in CASP13 prompts new routes for future assessments

Authors: Abriata, Luciano A.; Tamo, Giorgio E.; Dal Peraro, Matteo

Year: 2019

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/160666

Thesis A new age in protein design empowered by deep learning

Khakzad, Hamed; Igashov, Ilia; Schneuing, Arne et al. · 2024 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: A new age in protein design empowered by deep learning

Authors: Khakzad, Hamed; Igashov, Ilia; Schneuing, Arne; Goverde, Casper; Bronstein, Michael; Correia, Bruno

Year: 2024

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/204494

Thesis Computational drug development for membrane protein targets

Li, Haijian; Sun, Xiaolin; Cui, Wenqiang et al. · 2024 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Computational drug development for membrane protein targets

Authors: Li, Haijian; Sun, Xiaolin; Cui, Wenqiang; Xu, Marc; Dong, Junlin; Ekundayo, Babatunde Edukpe; Ni, Dongchun; Rao, Zhili; Guo, Liwei; Stahlberg, Henning; Yuan, Shuguang; Vogel, Pierre

Year: 2024

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/204906

Thesis A structural biology community assessment of AlphaFold2 applications

Akdel, M; Pires, DEV; Pardo, EP et al. · 2023 · University of Melbourne · DOI

Full title: A structural biology community assessment of AlphaFold2 applications

Authors: Akdel, M; Pires, DEV; Pardo, EP; Jänes, J; Zalevsky, AO; Mészáros, B; Bryant, P; Good, LL; Laskowski, RA; Pozzati, G; Shenoy, A; Zhu, W; Kundrotas, P; Serra, VR; Rodrigues, CHM; Dunham, AS; Burke, D; Borkakoti, N; Velankar, S; Frost, A; Basquin, J; Lindorff-Larsen, K; Bateman, A; Kajava, AV; Valencia, A; Ovchinnikov, S; Durairaj, J; Ascher, DB; Thornton, JM; Davey, NE; Stein, A; Elofsson, A; Croll, TI; Beltrao, P

Year: 2023

Venue: University of Melbourne

DOI: https://hdl.handle.net/11343/327156

Thesis AI-driven GPCR analysis, engineering, and targeting

Velloso, JPL; Kovacs, AS; Pires, DEV et al. · 2024 · University of Melbourne · DOI

Full title: AI-driven GPCR analysis, engineering, and targeting

Authors: Velloso, JPL; Kovacs, AS; Pires, DEV; Ascher, DB

Year: 2024

Venue: University of Melbourne

DOI: https://hdl.handle.net/11343/343886

Thesis Critical assessment of approaches for molecular docking to elucidate associations of HLA alleles with adverse drug reactions

Ramsbottom, Kerry A; Carr, Daniel F; Jones, Andrew R et al. · 2018 · University of Liverpool · DOI

Full title: Critical assessment of approaches for molecular docking to elucidate associations of HLA alleles with adverse drug reactions

Authors: Ramsbottom, Kerry A; Carr, Daniel F; Jones, Andrew R; Rigden, Daniel J

Year: 2018

Venue: University of Liverpool

DOI: https://livrepository.liverpool.ac.uk/3026378/1/Ramsbottom_et_al_revised_marked.docx

Thesis Assessing the utility of CASP14 models for molecular replacement

Millan, Claudia; Keegan, Ronan M; Pereira, Joana et al. · 2021 · University of Liverpool · DOI

Full title: Assessing the utility of CASP14 models for molecular replacement

Authors: Millan, Claudia; Keegan, Ronan M; Pereira, Joana; Sammito, Massimo D; Simpkin, Adam J; McCoy, Airlie J; Lupas, Andrei N; Hartmann, Marcus D; Rigden, Daniel J; Read, Randy J

Year: 2021

Venue: University of Liverpool

DOI: oai:livrepository.liverpool.ac.uk:3145937

Thesis Evaluation of model refinement in CASP14

Simpkin, Adam J; Sanchez Rodriguez, Filomeno; Mesdaghi, Shahram et al. · 2021 · University of Liverpool · DOI

Full title: Evaluation of model refinement in CASP14

Authors: Simpkin, Adam J; Sanchez Rodriguez, Filomeno; Mesdaghi, Shahram; Kryshtafovych, Andriy; Rigden, Daniel J

Year: 2021

Venue: University of Liverpool

DOI: oai:livrepository.liverpool.ac.uk:3138060

Thesis Using deep-learning predictions of inter-residue distances for model validation

Rodriguez, Filomeno Sanchez; Chojnowski, Grzegorz; Keegan, Ronan M et al. · 2022 · University of Liverpool · DOI

Full title: Using deep-learning predictions of inter-residue distances for model validation

Authors: Rodriguez, Filomeno Sanchez; Chojnowski, Grzegorz; Keegan, Ronan M; Rigden, Daniel J

Year: 2022

Venue: University of Liverpool

DOI: oai:livrepository.liverpool.ac.uk:3166536

Thesis High-accuracy protein structure prediction in CASP14

Pereira, Joana; Simpkin, Adam J; Hartmann, Marcus D et al. · 2021 · University of Liverpool · DOI

Full title: High-accuracy protein structure prediction in CASP14

Authors: Pereira, Joana; Simpkin, Adam J; Hartmann, Marcus D; Rigden, Daniel J; Keegan, Ronan M; Lupas, Andrei N

Year: 2021

Venue: University of Liverpool

DOI: oai:livrepository.liverpool.ac.uk:3129739

Thesis Benchmarking and improving artificial intelligence-aided high-throughput virtual screening methods for drug leads

Hao, Yang · 2024 · University of Liverpool · DOI

Full title: Benchmarking and improving artificial intelligence-aided high-throughput virtual screening methods for drug leads

Authors: Hao, Yang

Year: 2024

Venue: University of Liverpool

DOI: https://livrepository.liverpool.ac.uk/3187025/1/201529004_Oct2024.pdf

Thesis Extracting protein flexibility features from a pre-trained protein language model

Karlin, Vera · 2024 · Lund University Student Papers · DOI

Full title: Extracting protein flexibility features from a pre-trained protein language model

Authors: Karlin, Vera

Year: 2024

Venue: Lund University Student Papers

DOI: http://lup.lub.lu.se/student-papers/record/9146229

Thesis Benchmarking a memetic algorithm for global all-atom protein-protein docking with backbone flexibility

Karlin, Vera · 2022 · Lund University Student Papers · DOI

Full title: Benchmarking a memetic algorithm for global all-atom protein-protein docking with backbone flexibility

Authors: Karlin, Vera

Year: 2022

Venue: Lund University Student Papers

DOI: http://lup.lub.lu.se/student-papers/record/9078600

Thesis Prediction of Allosteric Binding Modes in Homologous NMDA-Receptors

Sellerberg, Anton Julius · 2024 · Lund University Student Papers · DOI

Full title: Prediction of Allosteric Binding Modes in Homologous NMDA-Receptors

Authors: Sellerberg, Anton Julius

Year: 2024

Venue: Lund University Student Papers

DOI: http://lup.lub.lu.se/student-papers/record/9178601

Thesis Assessment of protein-protein interfaces using graph neural networks

Virupaksha, Yashwanth Reddy, author; Ben-Hur, Asa, advisor; Anderson, Charles W., committee member et al. · 2021 · Colorado State University · DOI

Full title: Assessment of protein-protein interfaces using graph neural networks

Authors: Virupaksha, Yashwanth Reddy, author; Ben-Hur, Asa, advisor; Anderson, Charles W., committee member; Adams, Henry Hugh, committee member

Year: 2021

Venue: Colorado State University

DOI: https://hdl.handle.net/10217/233751

Thesis Expanding the druggable proteome by integrating deep learning with molecular simulations to predict cryptic pockets

Meller, Artur · 2025 · Washington University in St. Louis · DOI

Full title: Expanding the druggable proteome by integrating deep learning with molecular simulations to predict cryptic pockets

Authors: Meller, Artur

Year: 2025

Venue: Washington University in St. Louis

DOI: https://openscholarship.wustl.edu/art_sci_etds/3508

Thesis Leveraging protein dynamics to drug filovirus protein-nucleic acid interactions using simulations and experiments

Cruz, Matthew Alberto · 2023 · Washington University in St. Louis · DOI

Full title: Leveraging protein dynamics to drug filovirus protein-nucleic acid interactions using simulations and experiments

Authors: Cruz, Matthew Alberto

Year: 2023

Venue: Washington University in St. Louis

DOI: https://openscholarship.wustl.edu/art_sci_etds/2988

Thesis Combining computer simulations and deep learning to understand and predict protein structural dynamics

Ward, Michael D. · 2022 · Washington University in St. Louis · DOI

Full title: Combining computer simulations and deep learning to understand and predict protein structural dynamics

Authors: Ward, Michael D.

Year: 2022

Venue: Washington University in St. Louis

DOI: https://openscholarship.wustl.edu/art_sci_etds/2729

Thesis Developing novel scoring functions for protein-ligand docking using machine learning

Boyles, F · 2020 · University of Oxford - ORA · DOI

Full title: Developing novel scoring functions for protein-ligand docking using machine learning

Authors: Boyles, F

Year: 2020

Venue: University of Oxford - ORA

DOI: oai:ora.ox.ac.uk:uuid:2255ad26-71dd-4470-a13d-e4f30e8a4a6a

Thesis Deep learning approaches for pre-clinical drug discovery

Imrie, FM · 2021 · University of Oxford - ORA · DOI

Full title: Deep learning approaches for pre-clinical drug discovery

Authors: Imrie, FM

Year: 2021

Venue: University of Oxford - ORA

DOI: oai:ora.ox.ac.uk:uuid:129fee63-66e6-45f7-b962-dddafaa7ff5d

Thesis Integrative approaches in fragment-based drug discovery

Grosjean, H · 2023 · University of Oxford - ORA · DOI

Full title: Integrative approaches in fragment-based drug discovery

Authors: Grosjean, H

Year: 2023

Venue: University of Oxford - ORA

DOI: oai:ora.ox.ac.uk:uuid:375f6970-56bb-4868-a679-567db9b4bd7a

Thesis Deep learning applications in structure-based drug discovery

Meli, R · 2022 · University of Oxford - ORA · DOI

Full title: Deep learning applications in structure-based drug discovery

Authors: Meli, R

Year: 2022

Venue: University of Oxford - ORA

DOI: oai:ora.ox.ac.uk:uuid:c5c215a8-a29b-498d-b8ca-c70131df1dd4

Thesis Fragment hotspot mapping to drive the rational elaboration of fragment screening hits

Smilova, M · 2022 · University of Oxford - ORA · DOI

Full title: Fragment hotspot mapping to drive the rational elaboration of fragment screening hits

Authors: Smilova, M

Year: 2022

Venue: University of Oxford - ORA

DOI: oai:ora.ox.ac.uk:uuid:7031168a-4744-4019-a220-d2583385a390

Thesis Deep learning algorithms for predicting association between antibody sequence, structure, and antibody properties

Schneider, CC · 2021 · University of Oxford - ORA · DOI

Full title: Deep learning algorithms for predicting association between antibody sequence, structure, and antibody properties

Authors: Schneider, CC

Year: 2021

Venue: University of Oxford - ORA

DOI: oai:ora.ox.ac.uk:uuid:7926940d-7235-4290-be20-d75b25845f47

Thesis Assessment of AlphaFold2 for Human Proteins via Residue Solvent Exposure

Bæk, Kristoffer T.; id_orcid 0000-0003-3243-3962; Kepp, Kasper P. et al. · 2022 · Technical University of Denmark (DTU) · DOI

Full title: Assessment of AlphaFold2 for Human Proteins via Residue Solvent Exposure

Authors: Bæk, Kristoffer T.; id_orcid 0000-0003-3243-3962; Kepp, Kasper P.; id_orcid 0000-0002-6754-7348

Year: 2022

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/42ada4c6-8626-40b5-a89a-dad374a10f2d

Thesis AI in antibody design

Høie, Magnus Haraldson · 2024 · Technical University of Denmark (DTU) · DOI

Full title: AI in antibody design

Authors: Høie, Magnus Haraldson

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/82fb9928-f06d-4cf9-959a-2a339d9c83e5

Thesis A comparative study of protein structure prediction tools for challenging targets:Snake venom toxins

Kalogeropoulos, Konstantinos; id_orcid 0000-0003-3907-9281; Bohn, Markus-Frederik et al. · 2024 · Technical University of Denmark (DTU) · DOI

Full title: A comparative study of protein structure prediction tools for challenging targets:Snake venom toxins

Authors: Kalogeropoulos, Konstantinos; id_orcid 0000-0003-3907-9281; Bohn, Markus-Frederik; Jenkins, David E.; Ledergerber, Jann; Sørensen, Christoffer V.; id_orcid 0000-0001-7727-936X; Hofmann, Nils; Wade, Jack; Fryer, Thomas; Nguyen, Giang Thi Tuyet; auf dem Keller, Ullrich; Laustsen, Andreas H.; id_orcid 0000-0001-6918-5574; Jenkins, Timothy P.; id_orcid 0000-0003-2979-5663

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/5e9f5f51-dcf7-473f-a1db-b9d7c52170c4

Thesis Prioritisation of active compounds that are novel scaffolds using a data-driven approach

Patel, H · 2018 · University of Oxford - ORA · DOI

Full title: Prioritisation of active compounds that are novel scaffolds using a data-driven approach

Authors: Patel, H

Year: 2018

Venue: University of Oxford - ORA

DOI: oai:ora.ox.ac.uk:uuid:f5d21bea-c518-44f3-81f6-3818b0f428b5

Thesis Foldy:An open-source web application for interactive protein structure analysis

Roberts, Jacob B.; Nava, Alberto A.; Pearson, Allison N. et al. · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Foldy:An open-source web application for interactive protein structure analysis

Authors: Roberts, Jacob B.; Nava, Alberto A.; Pearson, Allison N.; Incha, Matthew R.; Valencia, Luis E.; Ma, Melody; Rao, Abhay; Keasling, Jay D.

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/b09c3f5d-b8c5-4544-895d-37ceb6a5a81d

Thesis Beyond rotamers: a generative, probabilistic model of side chains in proteins

Harder, Tim; Boomsma, Wouter; Paluszewski, Martin et al. · 2010 · Technical University of Denmark (DTU) · DOI

Full title: Beyond rotamers: a generative, probabilistic model of side chains in proteins

Authors: Harder, Tim; Boomsma, Wouter; Paluszewski, Martin; Frellsen, Jes; Johansson, Kristoffer Enøe; Hamelryck, Thomas

Year: 2010

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/d9e32eca-f2d9-4bcb-964e-421d2a42b288

Thesis AbEpiTope-1.0:Improved antibody target prediction by use of AlphaFold and inverse folding

Clifford, Joakim Nøddeskov; Richardson, Eve; Peters, Bjoern et al. · 2025 · Technical University of Denmark (DTU) · DOI

Full title: AbEpiTope-1.0:Improved antibody target prediction by use of AlphaFold and inverse folding

Authors: Clifford, Joakim Nøddeskov; Richardson, Eve; Peters, Bjoern; Nielsen, Morten; id_orcid 0000-0001-7885-4311

Year: 2025

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/eea4b643-7b3b-4980-93c4-12ba861ebd97

Thesis AI is a viable alternative to high throughput screening:a 318-target study

Vazquez Uribe, Ruben; id_orcid 0000-0002-9800-0409 · 2024 · Technical University of Denmark (DTU) · DOI

Full title: AI is a viable alternative to high throughput screening:a 318-target study

Authors: Vazquez Uribe, Ruben; id_orcid 0000-0002-9800-0409

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/b2b77083-c4db-404e-8922-b3487257d283

Thesis NetTCR-struc, a structure driven approach for prediction of TCR-pMHC interactions

Deleuran, Sebastian N.; Nielsen, Morten; id_orcid 0000-0001-7885-4311 · 2025 · Technical University of Denmark (DTU) · DOI

Full title: NetTCR-struc, a structure driven approach for prediction of TCR-pMHC interactions

Authors: Deleuran, Sebastian N.; Nielsen, Morten; id_orcid 0000-0001-7885-4311

Year: 2025

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/3990a167-3c15-4dc3-9c87-cdcf43c19ac9

Thesis Modelling SARS-CoV-2 spike-protein mutation effects on ACE2 binding

Thakur, Shivani; Verma, Rajaneesh Kumar; Kepp, Kasper Planeta et al. · 2023 · Technical University of Denmark (DTU) · DOI

Full title: Modelling SARS-CoV-2 spike-protein mutation effects on ACE2 binding

Authors: Thakur, Shivani; Verma, Rajaneesh Kumar; Kepp, Kasper Planeta; id_orcid 0000-0002-6754-7348; Mehra, Rukmankesh

Year: 2023

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/13ffb5a6-e8a7-4f5d-a5a9-519e27ed6f1b

Thesis Structural heterogeneity and precision of implications drawn from cryo-electron microscopy structures:SARS-CoV-2 spike-protein mutations as a test case

Mehra, Rukmankesh; Kepp, Kasper P.; id_orcid 0000-0002-6754-7348 · 2022 · Technical University of Denmark (DTU) · DOI

Full title: Structural heterogeneity and precision of implications drawn from cryo-electron microscopy structures:SARS-CoV-2 spike-protein mutations as a test case

Authors: Mehra, Rukmankesh; Kepp, Kasper P.; id_orcid 0000-0002-6754-7348

Year: 2022

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/1d5242f4-63af-4ee6-abc1-0fe6c1a96a9c

Thesis NetTCR-struc, a structure driven approach for prediction of TCR-pMHC interactions

Deleuran, Sebastian N.; Nielsen, Morten; id_orcid 0000-0001-7885-4311 · 2025 · Technical University of Denmark (DTU) · DOI

Full title: NetTCR-struc, a structure driven approach for prediction of TCR-pMHC interactions

Authors: Deleuran, Sebastian N.; Nielsen, Morten; id_orcid 0000-0001-7885-4311

Year: 2025

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/3990a167-3c15-4dc3-9c87-cdcf43c19ac9

Thesis AI is a viable alternative to high throughput screening:a 318-target study

Wallach, Izhar; Bernard, Denzil; Nguyen, Kong et al. · 2024 · Charles Sturt University - Research Output · DOI

Full title: AI is a viable alternative to high throughput screening:a 318-target study

Authors: Wallach, Izhar; Bernard, Denzil; Nguyen, Kong; Ho, Gregory; Morrison, Adrian; Stecula, Adrian; Rosnik, Andreana; O’Sullivan, Ann Marie; Davtyan, Aram; Samudio, Ben; Thomas, Bill; Worley, Brad; Butler, Brittany; Laggner, Christian; Thayer, Desiree; Moharreri, Ehsan; Friedland, Greg; Truong, Ha; van den Bedem, Henry; Ng, Ho Leung; Stafford, Kate; Sarangapani, Krishna; Giesler, Kyle; Ngo, Lien; Mysinger, Michael; Ahmed, Mostafa; Anthis, Nicholas J.; Henriksen, Niel; Gniewek, Pawel; Eckert, Sam; de Oliveira, Saulo; Suterwala, Shabbir; PrasadPrasad, Srimukh Veccham Krishna; Shek, Stefani; Contreras, Stephanie; Hare, Stephanie; Palazzo, Teresa; O’Brien, Terrence E.; Van Grack, Tessa; Williams, Tiffany; Chern, Ting Rong; Kenyon, Victor; Lee, Andreia H.; Cann, Andrew B.; Bergman, Bastiaan; Anderson, Brandon M.; Cox, Bryan D.; Warrington, Jeffrey M.; Sorenson, Jon M.; Goldenberg, Joshua M.; Young, Matthew A.; DeHaan, Nicholas; Pemberton, Ryan P.; Schroedl, Stefan; Abramyan, Tigran M.; Gupta, Tushita; Mysore, Venkatesh; Presser, Adam G.; Ferrando, Adolfo A.; Andricopulo, Adriano D.; Ghosh, Agnidipta; Ayachi, Aicha Gharbi; Mushtaq, Aisha; Shaqra, Ala M.; Toh, Alan Kie Leong; Smrcka, Alan V.; Ciccia, Alberto; de Oliveira, Aldo Sena; Sverzhinsky, Aleksandr; de Sousa, Alessandra Mara; Agoulnik, Alexander I.; Kushnir, Alexander; Freiberg, Alexander N.; Statsyuk, Alexander V.; Gingras, Alexandre R.; Degterev, Alexei; Tomilov, Alexey; Vrielink, Alice; Garaeva, Alisa A.; Bryant-Friedrich, Amanda; Caflisch, Amedeo; Patel, Amit K.; Rangarajan, Amith Vikram; Matheeussen, An; Battistoni, Andrea; Caporali, Andrea; Chini, Andrea; Ilari, Andrea; Mattevi, Andrea; Foote, Andrea Talbot; Trabocchi, Andrea; Stahl, Andreas; Herr, Andrew B.; Berti, Andrew; Freywald, Andrew; Reidenbach, Andrew G.; Lam, Andrew; Cuddihy, Andrew R.; White, Andrew; Taglialatela, Angelo; Ojha, Anil K.; Cathcart, Ann M.; Motyl, Anna A.L.; Borowska, Anna; D’Antuono, Anna; Hirsch, Anna K.H.; Porcelli, Anna Maria; Minakova, Anna; Montanaro, Anna; Müller, Anna; Fiorillo, Annarita; Virtanen, Anniina; O’Donoghue, Anthony J.; Del Rio Flores, Antonio; Garmendia, Antonio E.; Pineda-Lucena, Antonio; Panganiban, Antonito T.; Samantha, Ariela; Chatterjee, Arnab K.; Haas, Arthur L.; Paparella, Ashleigh S.; John, Ashley L.St; Prince, Ashutosh; ElSheikh, Assmaa; Apfel, Athena Marie; Colomba, Audrey; O’Dea, Austin; Diallo, Bakary N’tji; Ribeiro, Beatriz Murta Rezende Moraes; Bailey-Elkin, Ben A.; Edelman, Benjamin L.; Liou, Benjamin; Perry, Benjamin; Chua, Benjamin Soon Kai; Kováts, Benjámin; Englinger, Bernhard; Balakrishnan, Bijina; Gong, Bin; Agianian, Bogos; Pressly, Brandon; Salas, Brenda P.Medellin; Duggan, Brendan M.; Geisbrecht, Brian V.; Dymock, Brian W.; Morten, Brianna C.; Hammock, Bruce D.; Mota, Bruno Eduardo Fernandes; Dickinson, Bryan C.; Fraser, Cameron; Lempicki, Camille; Novina, Carl D.; Torner, Carles; Ballatore, Carlo; Bon, Carlotta; Chapman, Carly J.; Partch, Carrie L.; Chaton, Catherine T.; Huang, Chang; Yang, Chao Yie; Kahler, Charlene M.; Karan, Charles; Keller, Charles; Dieck, Chelsea L.; Huimei, Chen; Liu, Chen; Peltier, Cheryl; Mantri, Chinmay Kumar; Kemet, Chinyere Maat; Müller, Christa E.; Weber, Christian; Zeina, Christina M.; Muli, Christine S.; Morisseau, Christophe; Alkan, Cigdem; Reglero, Clara; Loy, Cody A.; Wilson, Cornelia M.; Myhr, Courtney; Arrigoni, Cristina; Paulino, Cristina; Santiago, César; Luo, Dahai; Tumes, Damon J.; Keedy, Daniel A.; Lawrence, Daniel A.; Chen, Daniel; Manor, Danny; Trader, Darci J.; Hildeman, David A.; Drewry, David H.; Dowling, David J.; Hosfield, David J.; Smith, David M.; Moreira, David; Siderovski, David P.; Shum, David; Krist, David T.; Riches, David W.H.; Ferraris, Davide Maria; Anderson, Deborah H.; Coombe, Deirdre R.; Welsbie, Derek S.; Hu, Di; Ortiz, Diana; Alramadhani, Dina; Zhang, Dingqiang; Chaudhuri, Dipayan; Slotboom, Dirk J.; Ronning, Donald R.; Lee, Donghan; Dirksen, Dorian; Shoue, Douglas A.; Zochodne, Douglas William; Krishnamurthy, Durga; Duncan, Dustin; Glubb, Dylan M.; Gelardi, Edoardo Luigi Maria; Hsiao, Edward C.; Lynn, Edward G.; Silva, Elany Barbosa; Aguilera, Elena; Lenci, Elena; Abraham, Elena Theres; Lama, Eleonora; Mameli, Eleonora; Leung, Elisa; Christensen, Emily M.; Mason, Emily R.; Petretto, Enrico; Trakhtenberg, Ephraim F.; Rubin, Eric J.; Strauss, Erick; Thompson, Erik W.; Cione, Erika; Lisabeth, Erika Mathes; Fan, Erkang; Kroon, Erna Geessien; Jo, Eunji; García-Cuesta, Eva M.; Glukhov, Evgenia; Gavathiotis, Evripidis; Yu, Fang; Xiang, Fei; Leng, Fenfei; Wang, Feng; Ingoglia, Filippo; van den Akker, Focco; Borriello, Francesco; Vizeacoumar, Franco J.; Luh, Frank; Buckner, Frederick S.; Vizeacoumar, Frederick S.; Bdira, Fredj Ben; Svensson, Fredrik; Rodriguez, G. Marcela; Bognár, Gabriella; Lembo, Gaia; Zhang, Gang; Dempsey, Garrett; Eitzen, Gary; Mayer, Gaétan; Greene, Geoffrey L.; Garcia, George A.; Lukacs, Gergely L.; Prikler, Gergely; Parico, Gian Carlo G.; Colotti, Gianni; De Keulenaer, Gilles; Cortopassi, Gino; Roti, Giovanni; Girolimetti, Giulia; Fiermonte, Giuseppe; Gasparre, Giuseppe; Leuzzi, Giuseppe; Dahal, Gopal; Michlewski, Gracjan; Conn, Graeme L.; Stuchbury, Grant David; Bowman, Gregory R.; Popowicz, Grzegorz Maria; Veit, Guido; de Souza, Guilherme Eduardo; Akk, Gustav; Caljon, Guy; Alvarez, Guzmán; Rucinski, Gwennan; Lee, Gyeongeun; Cildir, Gökhan; Li, Hai; Breton, Hairol E.; Jafar-Nejad, Hamed; Zhou, Han; Moore, Hannah P.; Tilford, Hannah; Yuan, Haynes; Shim, Heesung; Wulff, Heike; Hoppe, Heinrich; Chaytow, Helena; Tam, Heng Keat; Van Remmen, Holly; Xu, Hongyang; Debonsi, Hosana Maria; Lieberman, Howard B.; Jung, Hoyoung; Fan, Hua Ying; Feng, Hui; Zhou, Hui; Kim, Hyeong Jun; Greig, Iain R.; Caliandro, Ileana; Corvo, Ileana; Arozarena, Imanol; Mungrue, Imran N.; Verhamme, Ingrid M.; Qureshi, Insaf Ahmed; Lotsaris, Irina; Cakir, Isin; Perry, J. Jefferson P.; Kwiatkowski, Jacek; Boorman, Jacob; Ferreira, Jacob; Fries, Jacob; Kratz, Jadel Müller; Miner, Jaden; Siqueira-Neto, Jair L.; Granneman, James G.; Ng, James; Shorter, James; Voss, Jan Hendrik; Gebauer, Jan M.; Chuah, Janelle; Mousa, Jarrod J.; Maynes, Jason T.; Evans, Jay D.; Dickhout, Jeffrey; MacKeigan, Jeffrey P.; Jossart, Jennifer N.; Zhou, Jia; Lin, Jiabei; Xu, Jiake; Wang, Jianghai; Zhu, Jiaqi; Liao, Jiayu; Xu, Jingyi; Zhao, Jinshi; Lin, Jiusheng; Lee, Jiyoun; Reis, Joana; Stetefeld, Joerg; Bruning, John B.; Bruning, John Burt; Coles, John G.; Tanner, John J.; Pascal, John M.; So, Jonathan; Pederick, Jordan L.; Costoya, Jose A.; Rayman, Joseph B.; Maciag, Joseph J.; Nasburg, Joshua Alexander; Gruber, Joshua J.; Finkelstein, Joshua M.; Watkins, Joshua; Rodríguez-Frade, José Miguel; Arias, Juan Antonio Sanchez; Lasarte, Juan José; Oyarzabal, Julen; Milosavljevic, Julian; Cools, Julie; Lescar, Julien; Bogomolovas, Julijus; Wang, Jun; Kee, Jung Min; Kee, Jung Min; Liao, Junzhuo; Sistla, Jyothi C.; Abrahão, Jônatas Santos; Sishtla, Kamakshi; Francisco, Karol R.; Hansen, Kasper B.; Molyneaux, Kathleen A.; Cunningham, Kathryn A.; Martin, Katie R.; Gadar, Kavita; Ojo, Kayode K.; Wong, Keith S.; Wentworth, Kelly L.; Lai, Kent; Lobb, Kevin A.; Hopkins, Kevin M.; Parang, Keykavous; Machaca, Khaled; Pham, Kien; Ghilarducci, Kim; Sugamori, Kim S.; McManus, Kirk James; Musta, Kirsikka; Faller, Kiterie M.E.; Nagamori, Kiyo; Mostert, Konrad J.; Korotkov, Konstantin V.; Liu, Koting; Smith, Kristiana S.; Sarosiek, Kristopher; Rohde, Kyle H.; Kim, Kyu Kwang; Lee, Kyung Hyeon; Pusztai, Lajos; Lehtiö, Lari; Haupt, Larisa M.; Cowen, Leah E.; Byrne, Lee J.; Su, Leila; Wert-Lamas, Leon; Puchades-Carrasco, Leonor; Chen, Lifeng; Malkas, Linda H.; Zhuo, Ling; Hedstrom, Lizbeth; Hedstrom, Lizbeth; Walensky, Loren D.; Antonelli, Lorenzo; Iommarini, Luisa; Whitesell, Luke; Randall, Lía M.; Fathallah, M. Dahmani; Nagai, Maira Harume; Kilkenny, Mairi Louise; Ben-Johny, Manu; Lussier, Marc P.; Windisch, Marc P.; Lolicato, Marco; Lolli, Marco Lucio; Vleminckx, Margot; Caroleo, Maria Cristina; Macias, Maria J.; Valli, Marilia; Barghash, Marim M.; Mellado, Mario; Tye, Mark A.; Wilson, Mark A.; Hannink, Mark; Ashton, Mark R.; Cerna, Mark Vincent C.dela; Giorgis, Marta; Safo, Martin K.; Maurice, Martin St; McDowell, Mary Ann; Pasquali, Marzia; Mehedi, Masfique; Serafim, Mateus Sá Magalhães; Soellner, Matthew B.; Alteen, Matthew G.; Champion, Matthew M.; Skorodinsky, Maxim; O’Mara, Megan L.; Bedi, Mel; Rizzi, Menico; Levin, Michael; Mowat, Michael; Jackson, Michael R.; Paige, Mikell; Al-Yozbaki, Minnatallah; Giardini, Miriam A.; Maksimainen, Mirko M.; De Luise, Monica; Hussain, Muhammad Saddam; Christodoulides, Myron; Stec, Natalia; Zelinskaya, Natalia; Van Pelt, Natascha; Merrill, Nathan M.; Singh, Nathanael; Kootstra, Neeltje A.; Singh, Neeraj; Gandhi, Neha S.; Chan, Nei Li; Trinh, Nguyen Mai; Schneider, Nicholas O.; Matovic, Nick; Horstmann, Nicola; Longo, Nicola; Bharambe, Nikhil; Rouzbeh, Nirvan; Mahmoodi, Niusha; Gumede, Njabulo Joyfull; Anastasio, Noelle C.; Khalaf, Noureddine Ben; Rabal, Obdulia; Kandror, Olga; Escaffre, Olivier; Silvennoinen, Olli; Bishop, Ozlem Tastan; Iglesias, Pablo; Sobrado, Pablo; Chuong, Patrick; O’Connell, Patrick; Martin-Malpartida, Pau; Mellor, Paul; Fish, Paul V.; Moreira, Paulo Otávio Lourenço; Zhou, Pei; Liu, Pengda; Liu, Pengda; Wu, Pengpeng; Agogo-Mawuli, Percy; Jones, Peter L.; Ngoi, Peter; Toogood, Peter; Ip, Philbert; von Hundelshausen, Philipp; Lee, Pil H.; Rowswell-Turner, Rachael B.; Balaña-Fouce, Rafael; Rocha, Rafael Eduardo Oliveira; Guido, Rafael V.C.; Ferreira, Rafaela Salgado; Agrawal, Rajendra K.; Harijan, Rajesh K.; Ramachandran, Rajesh; Verma, Rajkumar; Singh, Rakesh K.; Tiwari, Rakesh Kumar; Mazitschek, Ralph; Koppisetti, Rama K.; Dame, Remus T.; Douville, Renée N.; Austin, Richard C.; Taylor, Richard E.; Moore, Richard G.; Ebright, Richard H.; Angell, Richard M.; Yan, Riqiang; Kejriwal, Rishabh; Batey, Robert A.; Blelloch, Robert; Vandenberg, Robert J.; Hickey, Robert J.; Kelm, Robert J.; Lake, Robert J.; Bradley, Robert K.; Blumenthal, Robert M.; Solano, Roberto; Gierse, Robin Matthias; Viola, Ronald E.; McCarthy, Ronan R.; Reguera, Rosa Maria; Uribe, Ruben Vazquez; do Monte-Neto, Rubens Lima; Gorgoglione, Ruggiero; Cullinane, Ryan T.; Katyal, Sachin; Hossain, Sakib; Phadke, Sameer; Shelburne, Samuel A.; Geden, Sandra E.; Johannsen, Sandra; Wazir, Sarah; Legare, Scott; Landfear, Scott M.; Radhakrishnan, Senthil K.; Ammendola, Serena; Dzhumaev, Sergei; Seo, Seung Yong; Li, Shan; Zhou, Shan; Chu, Shaoyou; Chauhan, Shefali; Maruta, Shinsaku; Ashkar, Shireen R.; Shyng, Show Ling; Conticello, Silvestro G.; Buroni, Silvia; Garavaglia, Silvia; White, Simon J.; Zhu, Siran; Tsimbalyuk, Sofiya; Chadni, Somaia Haque; Byun, Soo Young; Park, Soonju; Xu, Sophia Q.; Banerjee, Sourav; Zahler, Stefan; Espinoza, Stefano; Gustincich, Stefano; Sainas, Stefano; Celano, Stephanie L.; Capuzzi, Stephen J.; Waggoner, Stephen N.; Poirier, Steve; Olson, Steven H.; Marx, Steven O.; Van Doren, Steven R.; Sarilla, Suryakala; Brady-Kalnay, Susann M.; Dallman, Sydney; Azeem, Syeda Maryam; Teramoto, Tadahisa; Mehlman, Tamar; Swart, Tarryn; Abaffy, Tatjana; Akopian, Tatos; Haikarainen, Teemu; Moreda, Teresa Lozano; Ikegami, Tetsuro; Teixeira, Thaiz Rodrigues; Jayasinghe, Thilina D.; Gillingwater, Thomas H.; Kampourakis, Thomas; Richardson, Timothy I.; Herdendorf, Timothy J.; Kotzé, Timothy J.; O’Meara, Timothy R.; Corson, Timothy W.; Hermle, Tobias; Ogunwa, Tomisin Happy; Lan, Tong; Su, Tong; Banjo, Toshihiro; O’Mara, Tracy A.; Chou, Tristan; Chou, Tsui Fen; Baumann, Ulrich; Desai, Umesh R.; Pai, Vaibhav P.; Thai, Van Chi; Tandon, Vasudha; Banerji, Versha; Robinson, Victoria L.; Gunasekharan, Vignesh; Namasivayam, Vigneshwaran; Segers, Vincent F.M.; Maranda, Vincent; Dolce, Vincenza; Maltarollo, Vinícius Gonçalves; Scoffone, Viola Camilla; Woods, Virgil A.; Ronchi, Virginia Paola; Van Hung Le, Vuong; Clayton, W. Brent; Lowther, W. Todd; Houry, Walid A.; Li, Wei; Tang, Weiping; Zhang, Wenjun; Van Voorhis, Wesley C.; Donaldson, William A.; Hahn, William C.; Kerr, William G.; Gerwick, William H.; Bradshaw, William J.; Foong, Wuen Ee; Blanchet, Xavier; Wu, Xiaoyang; Lu, Xin; Qi, Xin; Xu, Xin; Yu, Xinfang; Qin, Xingping; Wang, Xingyou; Yuan, Xinrui; Zhang, Xu; Zhang, Yan Jessie; Hu, Yanmei; Aldhamen, Yasser Ali; Chen, Yicheng; Li, Yihe; Sun, Ying; Zhu, Yini; Gupta, Yogesh K.; Pérez-Pertejo, Yolanda; Li, Yong; Tang, Young; He, Yuan; Tse-Dinh, Yuk Ching; Sidorova, Yulia A.; Yen, Yun; Li, Yunlong; Frangos, Zachary J.; Chung, Zara; Su, Zhengchen; Wang, Zhenghe; Zhang, Zhiguo; Liu, Zhongle; Inde, Zintis; Artía, Zoraima; Heifets, Abraham

Year: 2024

Venue: Charles Sturt University - Research Output

DOI: https://researchoutput.csu.edu.au/en/publications/8ba2409a-e69c-4301-aef1-cfe88f538593

Thesis Assessment of AlphaFold2 for Human Proteins via Residue Solvent Exposure

Bæk, Kristoffer T.; id_orcid 0000-0003-3243-3962; Kepp, Kasper P. et al. · 2022 · Technical University of Denmark (DTU) · DOI

Full title: Assessment of AlphaFold2 for Human Proteins via Residue Solvent Exposure

Authors: Bæk, Kristoffer T.; id_orcid 0000-0003-3243-3962; Kepp, Kasper P.; id_orcid 0000-0002-6754-7348

Year: 2022

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/42ada4c6-8626-40b5-a89a-dad374a10f2d

Thesis Assessing AF2's ability to predict structural ensembles of proteins

Riccabona, Jakob R.; Spoendlin, Fabian C.; Fischer, Anna-Lena M et al. · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Assessing AF2's ability to predict structural ensembles of proteins

Authors: Riccabona, Jakob R.; Spoendlin, Fabian C.; Fischer, Anna-Lena M; Loeffler, Johannes R.; Quoika, Patrick K.; Jenkins, Timothy P.; id_orcid 0000-0003-2979-5663; Ferguson, James A.; Smorodina, Eva; Laustsen, Andreas H.; id_orcid 0000-0001-6918-5574; Greiff, Victor; Forli, Stefano; Ward, Andrew B.; Deane, Charlotte M.; Fernández-Quintero, Monica L.

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/1e81b6ba-12c9-4cba-a2c1-a3aadec56c16

Thesis Deorphanizing Peptides Using Structure Prediction

Teufel, Felix; Refsgaard, Jan C.; Kasimova, Marina A. et al. · 2023 · Technical University of Denmark (DTU) · DOI

Full title: Deorphanizing Peptides Using Structure Prediction

Authors: Teufel, Felix; Refsgaard, Jan C.; Kasimova, Marina A.; Deibler, Kristine; Madsen, Christian T.; Stahlhut, Carsten; Grønborg, Mads; Winther, Ole; id_orcid 0000-0002-1966-3205; Madsen, Dennis

Year: 2023

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/57a10165-fd46-4926-a58a-668effd5dde6

Thesis A comparative study of protein structure prediction tools for challenging targets:Snake venom toxins

Kalogeropoulos, Konstantinos; id_orcid 0000-0003-3907-9281; Bohn, Markus-Frederik et al. · 2024 · Technical University of Denmark (DTU) · DOI

Full title: A comparative study of protein structure prediction tools for challenging targets:Snake venom toxins

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/5e9f5f51-dcf7-473f-a1db-b9d7c52170c4

Thesis AI is a viable alternative to high throughput screening:a 318-target study

Wallach, Izhar; Bernard, Denzil; Nguyen, Kong et al. · 2024 · Charles Sturt University - Research Output · DOI

Full title: AI is a viable alternative to high throughput screening:a 318-target study

Year: 2024

Venue: Charles Sturt University - Research Output

DOI: https://researchoutput.csu.edu.au/en/publications/8ba2409a-e69c-4301-aef1-cfe88f538593

Thesis AI in antibody design

Høie, Magnus Haraldson · 2024 · Technical University of Denmark (DTU) · DOI

Full title: AI in antibody design

Authors: Høie, Magnus Haraldson

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/82fb9928-f06d-4cf9-959a-2a339d9c83e5

Thesis Beyond rotamers:a generative, probabilistic model of side chains in proteins

Harder, Tim; Boomsma, Wouter Krogh; Paluszewski, Martin et al. · 2010 · University of Copenhagen · DOI

Full title: Beyond rotamers:a generative, probabilistic model of side chains in proteins

Authors: Harder, Tim; Boomsma, Wouter Krogh; Paluszewski, Martin; Frellsen, Jes; Johansson, Kristoffer Enøe; Hamelryck, Thomas Wim

Year: 2010

Venue: University of Copenhagen

DOI: https://researchprofiles.ku.dk/da/publications/5202ea9b-4f1c-4d70-95b1-20fe1c6a787e

Thesis Ligand-induced conformational changes: Improved predictions of ligand binding conformations and affinities

Frimurer, T.M.; Peters, Günther H.J.; id_orcid 0000-0001-9754-2663 et al. · 2003 · Technical University of Denmark (DTU) · DOI

Full title: Ligand-induced conformational changes: Improved predictions of ligand binding conformations and affinities

Authors: Frimurer, T.M.; Peters, Günther H.J.; id_orcid 0000-0001-9754-2663; Iversen, L.F.; Andersen, H.S.; Moller, N.P.H.; Olsen, Ove Holger

Year: 2003

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/872a0694-00d5-4612-aa90-20b5ef5e59af

Thesis AbEpiTope-1.0:Improved antibody target prediction by use of AlphaFold and inverse folding

Clifford, Joakim Nøddeskov; Richardson, Eve; Peters, Bjoern et al. · 2025 · Technical University of Denmark (DTU) · DOI

Full title: AbEpiTope-1.0:Improved antibody target prediction by use of AlphaFold and inverse folding

Authors: Clifford, Joakim Nøddeskov; Richardson, Eve; Peters, Bjoern; Nielsen, Morten; id_orcid 0000-0001-7885-4311

Year: 2025

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/eea4b643-7b3b-4980-93c4-12ba861ebd97

Thesis DeepDock:Enhancing ligand-protein interaction prediction by a combination of ligand and structure information

Liao, Zhirui; You, Ronghui; Huang, Xiaodi et al. · 2020 · Charles Sturt University - Research Output · DOI

Full title: DeepDock:Enhancing ligand-protein interaction prediction by a combination of ligand and structure information

Authors: Liao, Zhirui; You, Ronghui; Huang, Xiaodi; id_orcid 0000-0002-6084-1851; Yao, Xiaojun; Huang, Tao; Zhu, Shanfeng

Year: 2020

Venue: Charles Sturt University - Research Output

DOI: https://researchoutput.csu.edu.au/en/publications/dc61f37f-d3b9-422f-92ba-89ff03380257

Thesis Beyond rotamers: a generative, probabilistic model of side chains in proteins

Harder, Tim; Boomsma, Wouter; Paluszewski, Martin et al. · 2010 · Technical University of Denmark (DTU) · DOI

Full title: Beyond rotamers: a generative, probabilistic model of side chains in proteins

Authors: Harder, Tim; Boomsma, Wouter; Paluszewski, Martin; Frellsen, Jes; Johansson, Kristoffer Enøe; Hamelryck, Thomas

Year: 2010

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/d9e32eca-f2d9-4bcb-964e-421d2a42b288

Thesis AI is a viable alternative to high throughput screening:a 318-target study

Vazquez Uribe, Ruben; id_orcid 0000-0002-9800-0409 · 2024 · Technical University of Denmark (DTU) · DOI

Full title: AI is a viable alternative to high throughput screening:a 318-target study

Authors: Vazquez Uribe, Ruben; id_orcid 0000-0002-9800-0409

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/b2b77083-c4db-404e-8922-b3487257d283

Thesis Foldy:An open-source web application for interactive protein structure analysis

Roberts, Jacob B.; Nava, Alberto A.; Pearson, Allison N. et al. · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Foldy:An open-source web application for interactive protein structure analysis

Authors: Roberts, Jacob B.; Nava, Alberto A.; Pearson, Allison N.; Incha, Matthew R.; Valencia, Luis E.; Ma, Melody; Rao, Abhay; Keasling, Jay D.

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/b09c3f5d-b8c5-4544-895d-37ceb6a5a81d

Thesis Computational Biology Tools for Identifying Specific Ligand Binding Residues for Novel Agrochemical and Drug Design

Pena Neshich, Izabella Agostinho; Nishimura, Leticia; Moraes, Fabio Rogerio de [UNESP] et al. · 2018 · Universidade Estadual Paulista (UNESP) · DOI

Full title: Computational Biology Tools for Identifying Specific Ligand Binding Residues for Novel Agrochemical and Drug Design

Authors: Pena Neshich, Izabella Agostinho; Nishimura, Leticia; Moraes, Fabio Rogerio de [UNESP]; Salim, Jose Augusto; Villalta-Romero, Fabian; Borro, Luiz; Yano, Inacio Henrique; Mazoni, Ivan; Tasic, Ljubica; Jardine, Jose Gilberto; Neshich, Goran

Year: 2018

Venue: Universidade Estadual Paulista (UNESP)

DOI: http://dx.doi.org/10.2174/1389203716666150505234923

Thesis Discovery and Characterization of a Cryptic Secondary Binding Site in the Molecular Chaperone HSP70

O’connor, Suzanne; Le Bihan, Yann-Vaï; Westwood, Isaac M. et al. · 2022 · Universidade Estadual Paulista (UNESP) · DOI

Full title: Discovery and Characterization of a Cryptic Secondary Binding Site in the Molecular Chaperone HSP70

Authors: O’connor, Suzanne; Le Bihan, Yann-Vaï; Westwood, Isaac M.; Liu, Manjuan; Mak, Oi Wei; Zazeri, Gabriel [UNESP]; Povinelli, Ana P. R. [UNESP]; Jones, Alan M.; van Montfort, Rob; Reynisson, Jóhannes; Collins, Ian

Year: 2022

Venue: Universidade Estadual Paulista (UNESP)

DOI: http://dx.doi.org/10.3390/molecules27030817

Thesis Molecular Docking with Trivialized Momentum and Riemannian Diffusion Models: RDM-Lite Dock

Mirzazadeh, Ghazal · 2025 · Georgia Institute of Technology · DOI

Full title: Molecular Docking with Trivialized Momentum and Riemannian Diffusion Models: RDM-Lite Dock

Authors: Mirzazadeh, Ghazal

Year: 2025

Venue: Georgia Institute of Technology

DOI: https://hdl.handle.net/1853/78297

Thesis A virtual screening framework based on the binding site selectivity for small molecule drug discovery

Che, Xinhao; Liu, Qilei; Yu, Fang et al. · 2024 · Hong Kong University of Science and Technology (HKUST) · DOI

Full title: A virtual screening framework based on the binding site selectivity for small molecule drug discovery

Authors: Che, Xinhao; Liu, Qilei; Yu, Fang; Zhang, Lei; Gani, Rafiqul

Year: 2024

Venue: Hong Kong University of Science and Technology (HKUST)

DOI: http://repository.hkust.edu.hk/ir/Record/1783.1-140102

Thesis Towards Stable Representations for Protein Interface Prediction

Gao, Ziqi; Liu, Zijing; Li, Yu et al. · 2024 · Hong Kong University of Science and Technology (HKUST) · DOI

Full title: Towards Stable Representations for Protein Interface Prediction

Authors: Gao, Ziqi; Liu, Zijing; Li, Yu; Li, Jia

Year: 2024

Venue: Hong Kong University of Science and Technology (HKUST)

DOI: http://repository.hkust.edu.hk/ir/Record/1783.1-148607

Thesis Prediction of Aptamer-Small-Molecule Interactions Using Metastable States from Multiple Independent Molecular Dynamics Simulations

Rodriguez Serrano, Alan Fernando; Hsing, I-ming · 2022 · Hong Kong University of Science and Technology (HKUST) · DOI

Full title: Prediction of Aptamer-Small-Molecule Interactions Using Metastable States from Multiple Independent Molecular Dynamics Simulations

Authors: Rodriguez Serrano, Alan Fernando; Hsing, I-ming

Year: 2022

Venue: Hong Kong University of Science and Technology (HKUST)

DOI: http://repository.hkust.edu.hk/ir/Record/1783.1-121765

Thesis Deep learning methods to find potential inhibitor fragments for proteins

Suarez Vasquez, Michael Alexander · 2021 · Hong Kong University of Science and Technology (HKUST) · DOI

Full title: Deep learning methods to find potential inhibitor fragments for proteins

Authors: Suarez Vasquez, Michael Alexander

Year: 2021

Venue: Hong Kong University of Science and Technology (HKUST)

DOI: http://repository.hkust.edu.hk/ir/Record/1783.1-114579

Thesis Proteome-wide structural analysis identifies warhead- and coverage-specific biases in cysteine-focused chemoproteomics

White, Matthew EH; Gil, Jesús; Tate, Edward W · 2023 · Imperial College London · DOI

Full title: Proteome-wide structural analysis identifies warhead- and coverage-specific biases in cysteine-focused chemoproteomics

Authors: White, Matthew EH; Gil, Jesús; Tate, Edward W

Year: 2023

Venue: Imperial College London

DOI: http://dx.doi.org/10.1016/j.chembiol.2023.06.021

Thesis Beware of simple methods for structure-based virtual screening: the critical importance of broader comparisons

Tran-Nguyen, Viet-Khoa; Ballester, Pedro · 2023 · Imperial College London · DOI

Full title: Beware of simple methods for structure-based virtual screening: the critical importance of broader comparisons

Authors: Tran-Nguyen, Viet-Khoa; Ballester, Pedro

Year: 2023

Venue: Imperial College London

DOI: https://pubs.acs.org/doi/10.1021/acs.jcim.3c00218

Thesis A practical guide to machine-learning scoring for structure-based virtual screening

Tran-Nguyen, Viet-Khoa; Junaid, Muhammad; Simeon, Saw et al. · 2024 · Imperial College London · DOI

Full title: A practical guide to machine-learning scoring for structure-based virtual screening

Authors: Tran-Nguyen, Viet-Khoa; Junaid, Muhammad; Simeon, Saw; Ballester, Pedro J

Year: 2024

Venue: Imperial College London

DOI: https://www.nature.com/articles/s41596-023-00885-w

Thesis Protein structure-based evaluation of missense variants: Resources, challenges and future directions.

David, Alessia; Sternberg, Michael JE · 2023 · Imperial College London · DOI

Full title: Protein structure-based evaluation of missense variants: Resources, challenges and future directions.

Authors: David, Alessia; Sternberg, Michael JE

Year: 2023

Venue: Imperial College London

DOI: https://www.ncbi.nlm.nih.gov/pubmed/37126977

Thesis Computational design of target-specific linear peptide binders with TransformerBeta

Zhao, Haowen; Aprile, Francesco; Bravi, Barbara · 2024 · Imperial College London · DOI

Full title: Computational design of target-specific linear peptide binders with TransformerBeta

Authors: Zhao, Haowen; Aprile, Francesco; Bravi, Barbara

Year: 2024

Venue: Imperial College London

DOI: http://hdl.handle.net/10044/1/116109

Thesis SCORCH2: a generalised heterogeneous consensus model for high-enrichment interaction-based virtual screening

Chen, Lin; Blay, Vincent; Ballester, Pedro et al. · 2025 · Imperial College London · DOI

Full title: SCORCH2: a generalised heterogeneous consensus model for high-enrichment interaction-based virtual screening

Authors: Chen, Lin; Blay, Vincent; Ballester, Pedro; Houston, Douglas R

Year: 2025

Venue: Imperial College London

DOI: https://hdl.handle.net/10044/1/122911

Thesis Data-centric challenges with the application and adoption of artificial intelligence for drug discovery

Ghislat, Ghita; Hernandez-Hernandez, Saiveth; Piyawajanusorn, Chayanit et al. · 2024 · Imperial College London · DOI

Full title: Data-centric challenges with the application and adoption of artificial intelligence for drug discovery

Authors: Ghislat, Ghita; Hernandez-Hernandez, Saiveth; Piyawajanusorn, Chayanit; Ballester, Pedro J

Year: 2024

Venue: Imperial College London

DOI: https://www.tandfonline.com/doi/full/10.1080/17460441.2024.2403639

Thesis Application of docking methodologies to modeled proteins

Singh, Amar; Dauzhenka, Taras; Kundrotas, Petras J et al. · 2020 · Imperial College London · DOI

Full title: Application of docking methodologies to modeled proteins

Authors: Singh, Amar; Dauzhenka, Taras; Kundrotas, Petras J; Sternberg, Michael JE; Vakser, Ilya A

Year: 2020

Venue: Imperial College London

DOI: http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000520757000001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=1ba7043ffcc86c417c072aa74d649202

Thesis Phyre2.2: a community resource for template-based protein structure prediction

Powell, Harold R; Islam, Suhail A; David, Alessia et al. · 2025 · Imperial College London · DOI

Full title: Phyre2.2: a community resource for template-based protein structure prediction

Authors: Powell, Harold R; Islam, Suhail A; David, Alessia; Sternberg, Michael JE

Year: 2025

Venue: Imperial College London

DOI: https://hdl.handle.net/10044/1/118419

Thesis Computational characterisation of protein interaction sites: from small ligand pockets to large domain interfaces

Vianello, Francesca · 2021 · Imperial College London · DOI

Full title: Computational characterisation of protein interaction sites: from small ligand pockets to large domain interfaces

Authors: Vianello, Francesca

Year: 2021

Venue: Imperial College London

DOI: http://hdl.handle.net/10044/1/89838

Thesis 3DLigandSite: Structure-based prediction of protein-ligand binding sites

McGreig, Jake; Uri, Hannah; Antczak, Magdalena et al. · 2022 · Imperial College London · DOI

Full title: 3DLigandSite: Structure-based prediction of protein-ligand binding sites

Authors: McGreig, Jake; Uri, Hannah; Antczak, Magdalena; Michaelis, Martin; Sternberg, Michael; Wass, Mark

Year: 2022

Venue: Imperial College London

DOI: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac250/6567476

Thesis Proteome-wide structure-based accessibility analysis of ligandable and detectable cysteines in chemoproteomic datasets

White, Matthew EH; Gil, Jesus; Tate, Edward W · 2025 · Imperial College London · DOI

Full title: Proteome-wide structure-based accessibility analysis of ligandable and detectable cysteines in chemoproteomic datasets

Authors: White, Matthew EH; Gil, Jesus; Tate, Edward W

Year: 2025

Venue: Imperial College London

DOI: https://hdl.handle.net/10044/1/120489

Thesis Can predicted protein 3D-structures provide reliable insights into whether missense variants are disease-associated?

Ittisoponpisan, Sirawit; Islam, Suhail; Khanna, Tarun et al. · 2019 · Imperial College London · DOI

Full title: Can predicted protein 3D-structures provide reliable insights into whether missense variants are disease-associated?

Authors: Ittisoponpisan, Sirawit; Islam, Suhail; Khanna, Tarun; Alhuzimi, Eman; David, Alessia; Sternberg, Michael

Year: 2019

Venue: Imperial College London

DOI: http://hdl.handle.net/10044/1/70153

Thesis SARS-CoV-2 3D database: Understanding the Coronavirus Proteome and Evaluating Possible Drug Targets.

Alsulami, Ali; Thomas, Sherine; Jamasb, Arian et al. · 2020 · University of Cambridge · DOI

Full title: SARS-CoV-2 3D database: Understanding the Coronavirus Proteome and Evaluating Possible Drug Targets.

Authors: Alsulami, Ali; Thomas, Sherine; Jamasb, Arian; Beaudoin, Christopher; Moghul, Ismail; Bannerman, Bridget; Copoiu, Liviu; Vedithi, Sundeep; Torres, pedro; Blundell, Tom

Year: 2020

Venue: University of Cambridge

DOI: https://www.repository.cam.ac.uk/handle/1810/315038

Thesis Accurate prediction of protein structures and interactions using a three-track neural network.

Baek, Minkyung; DiMaio, Frank; Anishchenko, Ivan et al. · 2021 · University of Cambridge · DOI

Full title: Accurate prediction of protein structures and interactions using a three-track neural network.

Authors: Baek, Minkyung; DiMaio, Frank; Anishchenko, Ivan; Dauparas, Justas; Ovchinnikov, Sergey; Lee, Gyu Rie; Wang, Jue; Cong, Qian; Kinch, Lisa N; Schaeffer, R Dustin; Millán, Claudia; Park, Hahnbeom; Adams, Carson; Glassman, Caleb R; DeGiovanni, Andy; Pereira, Jose H; Rodrigues, Andria V; van Dijk, Alberdina A; Ebrecht, Ana C; Opperman, Diederik J; Sagmeister, Theo; Buhlheller, Christoph; Pavkov-Keller, Tea; Rathinaswamy, Manoj K; Dalwadi, Udit; Yip, Calvin K; Burke, John E; Garcia, K Christopher; Grishin, Nick V; Adams, Paul D; Read, Randy J; Baker, David

Year: 2021

Venue: University of Cambridge

DOI: https://www.repository.cam.ac.uk/handle/1810/325197

Thesis Ligand Docking Methods to Recognize Allosteric Inhibitors for G-Protein-Coupled Receptors

Harini, K; Jayashree, S; Tiwari, Vikas et al. · 2021 · University of Cambridge · DOI

Full title: Ligand Docking Methods to Recognize Allosteric Inhibitors for G-Protein-Coupled Receptors

Authors: Harini, K; Jayashree, S; Tiwari, Vikas; Vishwanath, Sneha; Sowdhamini, Ramanathan

Year: 2021

Venue: University of Cambridge

DOI: https://www.repository.cam.ac.uk/handle/1810/330041

Thesis Evaluation of model refinement in CASP13.

Read, Randy J; Sammito, Massimo D; Kryshtafovych, Andriy et al. · 2019 · University of Cambridge · DOI

Full title: Evaluation of model refinement in CASP13.

Authors: Read, Randy J; Sammito, Massimo D; Kryshtafovych, Andriy; Croll, Tristan I

Year: 2019

Venue: University of Cambridge

DOI: https://www.repository.cam.ac.uk/handle/1810/295354

Thesis Network modularity and local environment similarity as descriptors of protein structure

Grant, William · 2020 · University of Cambridge · DOI

Full title: Network modularity and local environment similarity as descriptors of protein structure

Authors: Grant, William

Year: 2020

Venue: University of Cambridge

DOI: https://www.repository.cam.ac.uk/handle/1810/305324

Thesis AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination.

Terwilliger, Thomas C; Liebschner, Dorothee; Croll, Tristan I et al. · 2023 · University of Cambridge · DOI

Full title: AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination.

Authors: Terwilliger, Thomas C; Liebschner, Dorothee; Croll, Tristan I; Williams, Christopher J; McCoy, Airlie J; Poon, Billy K; Afonine, Pavel V; Oeffner, Robert D; Richardson, Jane S; Read, Randy J; Adams, Paul D

Year: 2023

Venue: University of Cambridge

DOI: https://www.repository.cam.ac.uk/handle/1810/361650

Thesis Structure-aware generation of drug-like molecules

Drotár, Pavol; Jamasb, Arian Rokkum; Day, Ben et al. · 2021 · University of Cambridge · DOI

Full title: Structure-aware generation of drug-like molecules

Authors: Drotár, Pavol; Jamasb, Arian Rokkum; Day, Ben; Cangea, Cătălina; Liò, Pietro

Year: 2021

Venue: University of Cambridge

DOI: https://www.repository.cam.ac.uk/handle/1810/331624

Thesis A structural biology community assessment of AlphaFold2 applications.

Akdel, Mehmet; Pires, Douglas EV; Pardo, Eduard Porta et al. · 2022 · University of Cambridge · DOI

Full title: A structural biology community assessment of AlphaFold2 applications.

Authors: Akdel, Mehmet; Pires, Douglas EV; Pardo, Eduard Porta; Jänes, Jürgen; Zalevsky, Arthur O; Mészáros, Bálint; Bryant, Patrick; Good, Lydia L; Laskowski, Roman A; Pozzati, Gabriele; Shenoy, Aditi; Zhu, Wensi; Kundrotas, Petras; Serra, Victoria Ruiz; Rodrigues, Carlos HM; Dunham, Alistair S; Burke, David; Borkakoti, Neera; Velankar, Sameer; Frost, Adam; Basquin, Jérôme; Lindorff-Larsen, Kresten; Bateman, Alex; Kajava, Andrey V; Valencia, Alfonso; Ovchinnikov, Sergey; Durairaj, Janani; Ascher, David B; Thornton, Janet M; Davey, Norman E; Stein, Amelie; Elofsson, Arne; Croll, Tristan I; Beltrao, Pedro

Year: 2022

Venue: University of Cambridge

DOI: https://www.repository.cam.ac.uk/handle/1810/344194

Thesis Computational Deorphaning of Mycobacterium tuberculosis Targets

Yamurai Bishi, Lorraine; Chaitanya Vedithi, Sundeep; L. Blundell, Tom et al. · 2021 · University of Cambridge · DOI

Full title: Computational Deorphaning of Mycobacterium tuberculosis Targets

Authors: Yamurai Bishi, Lorraine; Chaitanya Vedithi, Sundeep; L. Blundell, Tom; Chitima Mugumbate, Grace

Year: 2021

Venue: University of Cambridge

DOI: https://www.repository.cam.ac.uk/handle/1810/327787

Thesis AlphaFold predictions are valuable hypotheses, and accelerate but do not replace experimental structure determination

Terwilliger, Thomas C; Liebschner, Dorothee; Croll, Tristan I et al. · 2022 · University of Cambridge · DOI

Full title: AlphaFold predictions are valuable hypotheses, and accelerate but do not replace experimental structure determination

Year: 2022

Venue: University of Cambridge

DOI: https://www.repository.cam.ac.uk/handle/1810/344791

Thesis Biological and functional relevance of CASP predictions

Liu, Tianyun; Ish‐Shalom, Shirbi; Torng, Wen et al. · 2018 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Biological and functional relevance of CASP predictions

Authors: Liu, Tianyun; Ish‐Shalom, Shirbi; Torng, Wen; Lafita, Aleix; Bock, Christian; Mort, Matthew; Cooper, David N.; Bliven, Spencer; Capitani, Guido; Mooney, Sean D.; Altman, Russ B.

Year: 2018

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/245186

Thesis Prediction of Inhibitory Activity against the MATE1 Transporter via Combined Fingerprint- and Physics-Based Machine Learning Models.

Handa, Koichi; Sasaki, Shunta; Asano, Satoshi et al. · 2024 · University of Cambridge · DOI

Full title: Prediction of Inhibitory Activity against the MATE1 Transporter via Combined Fingerprint- and Physics-Based Machine Learning Models.

Authors: Handa, Koichi; Sasaki, Shunta; Asano, Satoshi; Kageyama, Michiharu; Iijima, Takeshi; Bender, Andreas

Year: 2024

Venue: University of Cambridge

DOI: https://www.repository.cam.ac.uk/handle/1810/373487

Thesis Artificial intelligence in drug discovery: recent advances and future perspectives

Jiménez-Luna, José; Grisoni, Francesca; id_orcid0000-0001-8552-6615 et al. · 2021 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Artificial intelligence in drug discovery: recent advances and future perspectives

Authors: Jiménez-Luna, José; Grisoni, Francesca; id_orcid0000-0001-8552-6615; Weskamp, Nils; Schneider, Gisbert; id_orcid0000-0001-8552-6615

Year: 2021

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/495078

Thesis Predicting multiple conformations via sequence clustering and AlphaFold2.

Wayment-Steele, Hannah K; Ojoawo, Adedolapo; Otten, Renee et al. · 2025 · University of Cambridge · DOI

Full title: Predicting multiple conformations via sequence clustering and AlphaFold2.

Authors: Wayment-Steele, Hannah K; Ojoawo, Adedolapo; Otten, Renee; Apitz, Julia M; Pitsawong, Warintra; Hömberger, Marc; Ovchinnikov, Sergey; Colwell, Lucy; Kern, Dorothee

Year: 2025

Venue: University of Cambridge

DOI: https://www.repository.cam.ac.uk/handle/1810/379729

Thesis A critical overview of computational approaches employed for COVID-19 drug discovery

Muratov, Eugene N.; Amaro, Rommie; Andrade, Carolina H. et al. · 2021 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: A critical overview of computational approaches employed for COVID-19 drug discovery

Authors: Muratov, Eugene N.; Amaro, Rommie; Andrade, Carolina H.; Brown, Nathan; Ekins, Sean; Fourches, Denis; Isayev, Olexandr; Kozakov, Dima; Medina-Franco, José L.; Merz, Kenneth M.; Oprea, Tudor I.; Poroikov, Vladimir; Schneider, Gisbert; id_orcid0000-0001-6706-1084; Todd, Matthew H.; Varnek, Alexandre; Winkler, David A.; Zakharov, Alexey V.; Cherkasov, Artem; Tropsha, Alexander

Year: 2021

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/496964

Thesis Towards a structurally resolved human protein interaction network

Burke, David F.; Bryant, Patrick; Barrio-Hernandez, Inigo et al. · 2021 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Towards a structurally resolved human protein interaction network

Authors: Burke, David F.; Bryant, Patrick; Barrio-Hernandez, Inigo; Memon, Danish; Pozzati, Gabriele; Shenoy, Aditi; Zhu, Wensi; Dunham, Alistair S.; Albanese, Pascal; Keller, Andrew; Scheltema, Richard A.; Bruce, James E.; Leitner, Alexander; Kundrotas, Petras; Beltrao, Pedro; id_orcid0000-0002-2724-7703; Elofsson, Arne

Year: 2021

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/531960

Thesis Towards a structurally resolved human protein interaction network

Burke, David F.; Bryant, Patrick; Barrio-Hernandez, Inigo et al. · 2023 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Towards a structurally resolved human protein interaction network

Year: 2023

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/600784

Thesis Trends in Deep Learning for Property-driven Drug Design

Born, Jannis; id_orcid0000-0001-8307-5670; Manica, Matteo · 2021 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Trends in Deep Learning for Property-driven Drug Design

Authors: Born, Jannis; id_orcid0000-0001-8307-5670; Manica, Matteo

Year: 2021

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/522032

Thesis A Deep-Learning Approach toward Rational Molecular Docking Protocol Selection

Jiménez-Luna, José; Cuzzolin, Alberto; Bolcato, Giovanni et al. · 2020 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: A Deep-Learning Approach toward Rational Molecular Docking Protocol Selection

Authors: Jiménez-Luna, José; Cuzzolin, Alberto; Bolcato, Giovanni; Sturlese, Mattia; Moro, Stefano

Year: 2020

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/418736

Thesis A structural biology community assessment of AlphaFold2 applications

Akdel, Mehmet; Pires, Douglas E. V.; Porta Pardo, Eduard et al. · 2022 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: A structural biology community assessment of AlphaFold2 applications

Authors: Akdel, Mehmet; Pires, Douglas E. V.; Porta Pardo, Eduard; Jänes, Jürgen; Zalevsky, Arthur O.; Mészáros, Bálint; Bryant, Patrick; Good, Lydia L.; Laskowski, Roman A.; Pozzati, Gabriele; Shenoy, Aditi; Zhu, Wensi; Kundrotas, Petras; Ruiz Serra, Victoria; Rodrigues, Carlos H. M.; Dunham, Alistair S.; Burke, David; Borkakoti, Neera; Velankar, Sameer; Frost, Adam; Beltrao, Pedro; id_orcid0000-0002-2724-7703; et al.

Year: 2022

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/582234

Thesis Characterization of conformationally heterogeneous proteins by electron paramagnetic resonance spectroscopy

Jeschke, Gunnar; id_orcid0000-0001-6853-8585 · 2025 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Characterization of conformationally heterogeneous proteins by electron paramagnetic resonance spectroscopy

Authors: Jeschke, Gunnar; id_orcid0000-0001-6853-8585

Year: 2025

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/731451

Thesis Structure-based drug design with geometric deep learning

Isert, Clemens; id_orcid0000-0002-4176-7887; Atz, Kenneth et al. · 2023 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Structure-based drug design with geometric deep learning

Authors: Isert, Clemens; id_orcid0000-0002-4176-7887; Atz, Kenneth; id_orcid0000-0002-4176-7887; Schneider, Gisbert; id_orcid0000-0002-4176-7887

Year: 2023

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/601192

Thesis Integrating Large-Scale Protein Structure Prediction into Human Genetics Research

Correa Marrero, Miguel; id_orcid0000-0002-3840-3273; Jänes, Jürgen et al. · 2024 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Integrating Large-Scale Protein Structure Prediction into Human Genetics Research

Authors: Correa Marrero, Miguel; id_orcid0000-0002-3840-3273; Jänes, Jürgen; Baptista, Delora; Beltrao, Pedro; id_orcid0000-0002-3840-3273

Year: 2024

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/692538

Thesis Protein Binding Site Representation in Latent Space

Lohmann, Frederieke; id_orcid0000-0001-8122-2980; Allenspach, Stephan et al. · 2025 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Protein Binding Site Representation in Latent Space

Authors: Lohmann, Frederieke; id_orcid0000-0001-8122-2980; Allenspach, Stephan; Atz, Kenneth; id_orcid0000-0001-8122-2980; Schiebroek, Carl C.G.; Hiss, Jan A.; Schneider, Gisbert; id_orcid0000-0001-8122-2980

Year: 2025

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/712925

Thesis Structure Prediction and Computational Protein Design for Efficient Biocatalysts and Bioactive Proteins

Buller, Rebecca; Damborsky, Jiri; Hilvert, Donald et al. · 2025 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Structure Prediction and Computational Protein Design for Efficient Biocatalysts and Bioactive Proteins

Authors: Buller, Rebecca; Damborsky, Jiri; Hilvert, Donald; Bornscheuer, Uwe T.

Year: 2025

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/710331

Thesis GNINA 1.3: the next increment in molecular docking with deep learning

McNutt, Andrew T.; Li, Yanjing; Meli, Rocco et al. · 2025 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: GNINA 1.3: the next increment in molecular docking with deep learning

Authors: McNutt, Andrew T.; Li, Yanjing; Meli, Rocco; id_orcid0000-0002-2845-3410; Aggarwal, Rishal; Koes, David Ryan

Year: 2025

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/727621

Thesis A comparative study of protein structure prediction tools for challenging targets: Snake venom toxins

Kalogeropoulos, Konstantinos; Bohn, Markus-Frederik; Jenkins, David E. et al. · 2024 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: A comparative study of protein structure prediction tools for challenging targets: Snake venom toxins

Authors: Kalogeropoulos, Konstantinos; Bohn, Markus-Frederik; Jenkins, David E.; Ledergerber, Jann; id_orcid0009-0004-9774-095X; Sørensen, Christoffer V.; Hofmann, Nils; Wade, Jack; Fryer, Thomas; Thi Tuyet Nguyen, Giang; auf dem Keller, Ulrich; Laustsen, Andreas H.; Jenkins, Timothy P.

Year: 2024

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/651400

Thesis Deep learning for protein structure prediction and design—progress and applications

Jänes, Jürgen; Beltrao, Pedro; id_orcid0000-0002-2724-7703 · 2024 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Deep learning for protein structure prediction and design—progress and applications

Authors: Jänes, Jürgen; Beltrao, Pedro; id_orcid0000-0002-2724-7703

Year: 2024

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/666110

Thesis Assignment of heteronuclear methyl-NMR spectrum of the 44 kDa protein MALT1 Casp-IgL3

Levkovets, Maria · 2022 · Lund University Student Papers · DOI

Full title: Assignment of heteronuclear methyl-NMR spectrum of the 44 kDa protein MALT1 Casp-IgL3

Authors: Levkovets, Maria

Year: 2022

Venue: Lund University Student Papers

DOI: http://lup.lub.lu.se/student-papers/record/9082520

Thesis Protein sequence information encodes more than the global minimum structure

Schwarz, D · 2021 · University of Oxford - ORA · DOI

Full title: Protein sequence information encodes more than the global minimum structure

Authors: Schwarz, D

Year: 2021

Venue: University of Oxford - ORA

DOI: oai:ora.ox.ac.uk:uuid:2ac6f12d-55d1-47cd-8f38-2973bf0678a4

Thesis How well do the substrates KISS the enzyme? Molecular docking program selection for feruloyl esterases

Udatha, D. B. R. K. Gupta; Sugaya, Nobuyoshi; Olsson, Lisbeth et al. · 2012 · Technical University of Denmark (DTU) · DOI

Full title: How well do the substrates KISS the enzyme? Molecular docking program selection for feruloyl esterases

Authors: Udatha, D. B. R. K. Gupta; Sugaya, Nobuyoshi; Olsson, Lisbeth; Panagiotou, Gianni

Year: 2012

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/95fc5cd9-f90e-4654-a171-a68acca429a5

Thesis Contacts-based prediction of binding affinity in protein–protein complexes

Vangone, Anna; Bonvin, Alexandre M J J · 2015 · Utrecht University · DOI

Full title: Contacts-based prediction of binding affinity in protein–protein complexes

Authors: Vangone, Anna; Bonvin, Alexandre M J J

Year: 2015

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/351637

Thesis MolScore: a scoring, evaluation and benchmarking framework for generative models in de novo drug design

Thomas, Morgan; O'Boyle, Noel M; Bender, Andreas et al. · 2024 · University of Cambridge · DOI

Full title: MolScore: a scoring, evaluation and benchmarking framework for generative models in de novo drug design

Authors: Thomas, Morgan; O'Boyle, Noel M; Bender, Andreas; De Graaf, Chris

Year: 2024

Venue: University of Cambridge

DOI: https://www.repository.cam.ac.uk/handle/1810/368980

Patent us-2004015299-a1

· 2004

Full title: us-2004015299-a1

Year: 2004

2. Data Extraction

0/231 extracted

Paper

One substrate many enzymes virtual screening uncovers missing genes of carnitine biosynthesis in human and mouse.

Malatesta, Marco; Fornasier, Emanuele; Di Salvo, Martino Luigi et al. · 2024

Full title: One substrate many enzymes virtual screening uncovers missing genes of carnitine biosynthesis in human and mouse.

DOI: https://doi.org/10.1038/s41467-024-47466-3

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Deep contrastive learning enables genome-wide virtual screening

Full title: Deep contrastive learning enables genome-wide virtual screening

DOI: https://doi.org/10.1101/2024.09.02.610777

Paper

TopoFormer: Multiscale Topology-enabled Structure-to-Sequence Transformer for Protein-Ligand Interaction Predictions

Wei, Guo‐Wei, Chen, Dong, Liu, Jian · 2024

Full title: TopoFormer: Multiscale Topology-enabled Structure-to-Sequence Transformer for Protein-Ligand Interaction Predictions

Authors: Wei, Guo‐Wei, Chen, Dong, Liu, Jian

DOI: https://doi.org/10.21203/rs.3.rs-3640878/v1

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Revolutionizing Medicinal Chemistry: The Application of Artificial Intelligence (AI) in Early Drug Discovery

Han, Ri, Yoon, Hongryul, Kim, Gahee, Lee, Hyundo, Lee, Yoonji · 2023

Full title: Revolutionizing Medicinal Chemistry: The Application of Artificial Intelligence (AI) in Early Drug Discovery

Authors: Han, Ri, Yoon, Hongryul, Kim, Gahee, Lee, Hyundo, Lee, Yoonji

DOI: https://doi.org/10.3390/ph16091259

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Machine Learning Empowering Drug Discovery: Applications, Opportunities and Challenges

Qi, Xin, Zhao, Yuanchun, Qi, Zhuang, Hou, Siyu, Chen, Jiajia · 2024

Full title: Machine Learning Empowering Drug Discovery: Applications, Opportunities and Challenges

Authors: Qi, Xin, Zhao, Yuanchun, Qi, Zhuang, Hou, Siyu, Chen, Jiajia

DOI: https://doi.org/10.3390/molecules29040903

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Fusing Sequence and Structural Knowledge by Heterogeneous Models to Accurately and Interpretively Predict Drug–Target Affinity

Zeng, Xin, Zhong, Kai-Yang, Jiang, Bei, Li, Yi · 2023

Full title: Fusing Sequence and Structural Knowledge by Heterogeneous Models to Accurately and Interpretively Predict Drug–Target Affinity

Authors: Zeng, Xin, Zhong, Kai-Yang, Jiang, Bei, Li, Yi

DOI: https://doi.org/10.3390/molecules28248005

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The Application of Machine Learning on Antibody Discovery and Optimization

Zheng, Jiayao, Wang, Yu, Qin, Liang, Cui, Lun, Wang, Liqun · 2024

Full title: The Application of Machine Learning on Antibody Discovery and Optimization

Authors: Zheng, Jiayao, Wang, Yu, Qin, Liang, Cui, Lun, Wang, Liqun

DOI: https://doi.org/10.3390/molecules29245923

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Non-Steroidal Anti-Inflammatory Drugs Are Inhibitors of the Intestinal Proton-Coupled Amino Acid Transporter (PAT1): Ibuprofen and Diclofenac Are Non-Translocated Inhibitors

Nielsen, Carsten Uhd, Jakobsen, Sebastian, Pedersen, Maria L. · 2025

Full title: Non-Steroidal Anti-Inflammatory Drugs Are Inhibitors of the Intestinal Proton-Coupled Amino Acid Transporter (PAT1): Ibuprofen and Diclofenac Are Non-Translocated Inhibitors

Authors: Nielsen, Carsten Uhd, Jakobsen, Sebastian, Pedersen, Maria L.

DOI: https://doi.org/10.3390/pharmaceutics17010049

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Computational Methods in the Design of Anticancer Drugs

Fantacuzzi, Marialuigia, Agamennone, Mariangela · 2024

Full title: Computational Methods in the Design of Anticancer Drugs

Authors: Fantacuzzi, Marialuigia, Agamennone, Mariangela

DOI: https://doi.org/10.3390/ph17040404

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Machine Learning and Artificial Intelligence in Therapeutics and Drug Development Life Cycle

Borkotoky, Subhomoi, Joshi, Amit, Kaushik, Vikas, Jha, Anupam Nath · 2022

Full title: Machine Learning and Artificial Intelligence in Therapeutics and Drug Development Life Cycle

Authors: Borkotoky, Subhomoi, Joshi, Amit, Kaushik, Vikas, Jha, Anupam Nath

DOI: https://doi.org/10.5772/intechopen.104753

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M Protein from Dengue virus oligomerizes to pentameric channel protein: in silico analysis study

Zeba, Ayesha, Sekar, K., Ganjiwale, Anjali · 2023

Full title: M Protein from Dengue virus oligomerizes to pentameric channel protein: in silico analysis study

Authors: Zeba, Ayesha, Sekar, K., Ganjiwale, Anjali

DOI: https://doi.org/10.5808/gi.23035

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Drug-Online: an online platform for drug-target interaction, affinity, and binding sites identification using deep learning

Zeng, Xin, Su, Guang-Peng, Li, Shujuan, Lv, Shuang‐Qing, Wen, Meng‐Liang, Li, Yi · 2024

Full title: Drug-Online: an online platform for drug-target interaction, affinity, and binding sites identification using deep learning

Authors: Zeng, Xin, Su, Guang-Peng, Li, Shujuan, Lv, Shuang‐Qing, Wen, Meng‐Liang, Li, Yi

DOI: https://doi.org/10.1186/s12859-024-05783-w

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Chemoinformatics and artificial intelligence colloquium: progress and challenges in developing bioactive compounds

Full title: Chemoinformatics and artificial intelligence colloquium: progress and challenges in developing bioactive compounds

DOI: https://doi.org/10.1186/s13321-022-00661-0

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Single-cell profiling of SLC family transporters: uncovering the role of SLC7A1 in osteosarcoma

Liao, Yan, Chen, Junkai, Yao, Hao, Zheng, Ting, Tu, Jian, Chen, Wei‐Dong, Guo, Zhen, Zou, Yutong, Wen, Lili, Xie, X. Sunney · 2025

Full title: Single-cell profiling of SLC family transporters: uncovering the role of SLC7A1 in osteosarcoma

Authors: Liao, Yan, Chen, Junkai, Yao, Hao, Zheng, Ting, Tu, Jian, Chen, Wei‐Dong, Guo, Zhen, Zou, Yutong, Wen, Lili, Xie, X. Sunney

DOI: https://doi.org/10.1186/s12967-025-06086-1

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Benchmarking AlphaFold ‐enabled molecular docking predictions for antibiotic discovery

Wong, Felix, Krishnan, Aarti, Zheng, Erica J., Stärk, H., Manson, Abigail L., Earl, Ashlee M., Jaakkola, Tommi, Collins, James J. · 2022

Full title: Benchmarking AlphaFold ‐enabled molecular docking predictions for antibiotic discovery

Authors: Wong, Felix, Krishnan, Aarti, Zheng, Erica J., Stärk, H., Manson, Abigail L., Earl, Ashlee M., Jaakkola, Tommi, Collins, James J.

DOI: https://doi.org/10.15252/msb.202211081

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Exploring the ability of machine learning-based virtual screening models to identify the functional groups responsible for binding

Hadfield, Thomas E., Scantlebury, Jack, Deane, Charlotte M. · 2023

Full title: Exploring the ability of machine learning-based virtual screening models to identify the functional groups responsible for binding

Authors: Hadfield, Thomas E., Scantlebury, Jack, Deane, Charlotte M.

DOI: https://doi.org/10.1186/s13321-023-00755-3

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Accurate Pocket Identification for Binding-Site-Agnostic Docking

Balytskyi, Yaroslav, Hubenko, Inna, Balytska, Alina, Kelly, Christopher V. · 2025

Full title: Accurate Pocket Identification for Binding-Site-Agnostic Docking

Authors: Balytskyi, Yaroslav, Hubenko, Inna, Balytska, Alina, Kelly, Christopher V.

DOI: https://doi.org/10.20944/preprints202502.0352.v2

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Fusing Sequence and Structural Knowledge by Heterogeneous Models to Accurately and Interpretively Predict Drug-Target Affinity

Zeng, Xin, Zhong, Kai-Yang, Jiang, Bei, Li, Yi · 2023

Full title: Fusing Sequence and Structural Knowledge by Heterogeneous Models to Accurately and Interpretively Predict Drug-Target Affinity

Authors: Zeng, Xin, Zhong, Kai-Yang, Jiang, Bei, Li, Yi

DOI: https://doi.org/10.20944/preprints202310.1539.v1

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FusionPDB: a unique knowledgebase of human fusion proteins of consistent annotation across genome/ transcript/ protein/ interaction levels

Kumar, Himansu, Tang, Lin-Ya, Yang, Chengyuan, Kim, Pora · 2022

Full title: FusionPDB: a unique knowledgebase of human fusion proteins of consistent annotation across genome/ transcript/ protein/ interaction levels

Authors: Kumar, Himansu, Tang, Lin-Ya, Yang, Chengyuan, Kim, Pora

DOI: https://doi.org/10.21203/rs.3.rs-2202839/v1

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Multimodal Protein Representation Learning and Target-aware Variational Auto-encoders for Protein-binding Ligand Generation

Ngo, Nhat Khang, Hy, Truong Son · 2023

Full title: Multimodal Protein Representation Learning and Target-aware Variational Auto-encoders for Protein-binding Ligand Generation

Authors: Ngo, Nhat Khang, Hy, Truong Son

DOI: https://doi.org/10.21203/rs.3.rs-3504792/v1

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Lira: Rotational Invariant Shape and Electrostatic Descriptors for Small Molecules and Protein Pockets based on Real Spherical Harmonics

Caires, Fernando R., Silva, Samuel Reghim, Veríssimo-Alves, Marcos, Pinheiro, Vitor B., Montalvão, Rinaldo W. · 2022

Full title: Lira: Rotational Invariant Shape and Electrostatic Descriptors for Small Molecules and Protein Pockets based on Real Spherical Harmonics

Authors: Caires, Fernando R., Silva, Samuel Reghim, Veríssimo-Alves, Marcos, Pinheiro, Vitor B., Montalvão, Rinaldo W.

DOI: https://doi.org/10.1101/2022.01.19.476747

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Fragment-Based Ligand Generation Guided By Geometric Deep Learning On Protein-Ligand Structure

Powers, Alexander S., Yu, Helen H., Suriana, Patricia, Dror, Ron O. · 2022

Full title: Fragment-Based Ligand Generation Guided By Geometric Deep Learning On Protein-Ligand Structure

Authors: Powers, Alexander S., Yu, Helen H., Suriana, Patricia, Dror, Ron O.

DOI: https://doi.org/10.1101/2022.03.17.484653

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A chronopharmacology-friendly multi-target therapeutics based on AI: the example of therapeutic hypothermia

Liu, Fei, Jiang, Xiangkang, Zhang, Mao · 2022

Full title: A chronopharmacology-friendly multi-target therapeutics based on AI: the example of therapeutic hypothermia

Authors: Liu, Fei, Jiang, Xiangkang, Zhang, Mao

DOI: https://doi.org/10.1101/2022.03.07.22271997

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Investigating the folding dynamics of NS2B protein of Zika virus

Kumar, Ankur, Kumar, Prateek, Mishra, Pushpendra Mani, Giri, Rajanish · 2022

Full title: Investigating the folding dynamics of NS2B protein of Zika virus

Authors: Kumar, Ankur, Kumar, Prateek, Mishra, Pushpendra Mani, Giri, Rajanish

DOI: https://doi.org/10.1101/2022.12.12.520106

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Exploring The Ability Of Machine Learning-Based Virtual Screening Models To Identify The Functional Groups Responsible For Binding

Hadfield, Thomas E., Scantlebury, Jack, Deane, Charlotte M. · 2023

Full title: Exploring The Ability Of Machine Learning-Based Virtual Screening Models To Identify The Functional Groups Responsible For Binding

Authors: Hadfield, Thomas E., Scantlebury, Jack, Deane, Charlotte M.

DOI: https://doi.org/10.1101/2023.04.29.538820

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Protein property prediction based on local environment by 3D equivariant convolutional neural networks

Chen, He, Cheng, Yifan, Dong, Jianqiang, Mao, Jie, Wang, Xin, Gao, Yuan, Li, Yuchao, Wang, Chengzhi, Wu, Qiong · 2024

Full title: Protein property prediction based on local environment by 3D equivariant convolutional neural networks

Authors: Chen, He, Cheng, Yifan, Dong, Jianqiang, Mao, Jie, Wang, Xin, Gao, Yuan, Li, Yuchao, Wang, Chengzhi, Wu, Qiong

DOI: https://doi.org/10.1101/2024.02.07.579261

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NRGRank: Coarse-grained structurally-informed ultra-massive virtual screening

DesCôteaux, Thomas, Najmanovich, Rafaël, Najmanovich, Rafael · 2025

Full title: NRGRank: Coarse-grained structurally-informed ultra-massive virtual screening

Authors: DesCôteaux, Thomas, Najmanovich, Rafaël, Najmanovich, Rafael

DOI: https://doi.org/10.1101/2025.02.17.638675

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Highly accurate protein structure prediction-based virtual docking pipeline accelerating the identification of anti-schistosomal compounds

Cheng, Wenjun, Gu, Mengjie, Wang, Yuepeng, Wang, Jing, Li, Shan, Chen, Gongwen, Chen, Xu, Oyeyemi, Oyetunde T., Hong, Yang, Hu, Wei, Wang, Jipeng · 2025

Full title: Highly accurate protein structure prediction-based virtual docking pipeline accelerating the identification of anti-schistosomal compounds

Authors: Cheng, Wenjun, Gu, Mengjie, Wang, Yuepeng, Wang, Jing, Li, Shan, Chen, Gongwen, Chen, Xu, Oyeyemi, Oyetunde T., Hong, Yang, Hu, Wei, Wang, Jipeng

DOI: https://doi.org/10.1101/2025.06.09.658570

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Attention-based approach to predict drug-target interactions across seven target superfamilies

Schulman, Aron, Rousu, Juho, Aittokallio, Tero, Tanoli, Ziaurrehman · 2024

Full title: Attention-based approach to predict drug-target interactions across seven target superfamilies

Authors: Schulman, Aron, Rousu, Juho, Aittokallio, Tero, Tanoli, Ziaurrehman

DOI: https://doi.org/10.1101/2024.03.20.585893

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Structure and dynamics of pteridine reductase 1: the key phenomena relevant to enzyme function and drug design

Panecka-Hofman, Joanna, Poehner, Ina · 2023

Full title: Structure and dynamics of pteridine reductase 1: the key phenomena relevant to enzyme function and drug design

Authors: Panecka-Hofman, Joanna, Poehner, Ina

DOI: https://doi.org/10.1007/s00249-023-01677-6

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Sequence-based drug design as a concept in computational drug design

Full title: Sequence-based drug design as a concept in computational drug design

DOI: https://doi.org/10.1038/s41467-023-39856-w

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A multi-targeted computational drug discovery approach for repurposing tetracyclines against monkeypox virus

Alandijany, Thamir A., El-Daly, Mai M., Tolah, Ahmed M., Bajrai, Leena H., Khateb, Aiah M., Kumar, Geethu S, Dubey, Amit, Dwivedi, Vivek Dhar, Azhar, Esam I. · 2023

Full title: A multi-targeted computational drug discovery approach for repurposing tetracyclines against monkeypox virus

Authors: Alandijany, Thamir A., El-Daly, Mai M., Tolah, Ahmed M., Bajrai, Leena H., Khateb, Aiah M., Kumar, Geethu S, Dubey, Amit, Dwivedi, Vivek Dhar, Azhar, Esam I.

DOI: https://doi.org/10.1038/s41598-023-41820-z

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Identification of potential modulators of IFITM3 by in-silico modeling and virtual screening

Tiwari, Vikas, Viswanath, Shruthi · 2022

Full title: Identification of potential modulators of IFITM3 by in-silico modeling and virtual screening

Authors: Tiwari, Vikas, Viswanath, Shruthi

DOI: https://doi.org/10.1038/s41598-022-20259-8

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Bioinformatics approach for discovery of potential lead compound of NSP6 of SARS-CoV-2 using structure based virtual screening and molecular dynamics simulations.

Salama, Mohammed M, Shafaa, Medhat W, El-Nagdy, Mohamed E, Hasan, Mohamed E · 2025

Full title: Bioinformatics approach for discovery of potential lead compound of NSP6 of SARS-CoV-2 using structure based virtual screening and molecular dynamics simulations.

Authors: Salama, Mohammed M, Shafaa, Medhat W, El-Nagdy, Mohamed E, Hasan, Mohamed E

DOI: https://doi.org/10.1038/s41598-025-22409-0

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Computing the relative binding affinity of ligands based on a pairwise binding comparison network

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DOI: https://doi.org/10.1038/s43588-023-00529-9

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Specialty grand challenges in theoretical modeling, structure prediction and design

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Full title: Specialty grand challenges in theoretical modeling, structure prediction and design

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DOI: https://doi.org/10.3389/fchbi.2025.1635423

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Chang, Liwei, Mondal, Arup, Pérez, Alberto · 2022

Full title: Towards rational computational peptide design

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DOI: https://doi.org/10.3389/fbinf.2022.1046493

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Target-driven machine learning-enabled virtual screening (TAME-VS) platform for early-stage hit identification

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Full title: Target-driven machine learning-enabled virtual screening (TAME-VS) platform for early-stage hit identification

Authors: Bian, Yuemin, Kwon, Jason J., Liu, Cong, Margiotta, Enrico, Shekhar, Mrinal, Gould, Alexandra E.

DOI: https://doi.org/10.3389/fmolb.2023.1163536

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Editorial: Structural studies of bacteria and viruses

Pastore, Annalisa · 2025

Full title: Editorial: Structural studies of bacteria and viruses

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DOI: https://doi.org/10.3389/fmolb.2025.1605596

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Potential Inhibitors of Lumpy Skin Disease’s Viral Protein (DNA Polymerase): A Combination of Bioinformatics Approaches

Zia, S. H., Sumon, Mahmudul Reza, Ashik, Md-Ashiqur, Basar, Abul, Lim, Sang Jin, Oh, Yeonsu, Park, Yung Chul, Rahman, Md. Mafizur · 2024

Full title: Potential Inhibitors of Lumpy Skin Disease’s Viral Protein (DNA Polymerase): A Combination of Bioinformatics Approaches

Authors: Zia, S. H., Sumon, Mahmudul Reza, Ashik, Md-Ashiqur, Basar, Abul, Lim, Sang Jin, Oh, Yeonsu, Park, Yung Chul, Rahman, Md. Mafizur

DOI: https://doi.org/10.3390/ani14091283

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From Code to Cure: The Impact of Artificial Intelligence in Biomedical Applications

Gromiha, M. Michael, Preethi, P., Pandey, Medha · 2024

Full title: From Code to Cure: The Impact of Artificial Intelligence in Biomedical Applications

Authors: Gromiha, M. Michael, Preethi, P., Pandey, Medha

DOI: https://doi.org/10.3390/biomedinformatics4010030

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Öğüt, Eren · 2025

Full title: Artificial Intelligence in Clinical Medicine: Challenges Across Diagnostic Imaging, Clinical Decision Support, Surgery, Pathology, and Drug Discovery

Authors: Öğüt, Eren

DOI: https://doi.org/10.3390/clinpract15090169

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Trends and Applications in Computationally Driven Drug Repurposing

Pinzi, Luca, Rastelli, Giulio · 2023

Full title: Trends and Applications in Computationally Driven Drug Repurposing

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DOI: https://doi.org/10.3390/ijms242216511

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A divide and conquer approach (DACA) to predict high fidelity structure of large multidomain protein BRWD1

Mondal, Rajkrishna; Mandal, Malay; Lahiri, Tapobrata · 2023

Full title: A divide and conquer approach (DACA) to predict high fidelity structure of large multidomain protein BRWD1

Authors: Mondal, Rajkrishna; Mandal, Malay; Lahiri, Tapobrata

DOI: https://doi.org/10.1101/2023.07.10.548240

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Hybrid protein-ligand binding residue prediction with protein language models: Does the structure matter?

Gamouh, Hamza; Novotný, Marián; Hoksza, David · 2023

Full title: Hybrid protein-ligand binding residue prediction with protein language models: Does the structure matter?

Authors: Gamouh, Hamza; Novotný, Marián; Hoksza, David

DOI: https://doi.org/10.1101/2023.08.11.553028

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AF2BIND: Predicting ligand-binding sites using the pair representation of AlphaFold2

Gazizov, Artem; Lian, Anna; Goverde, Casper A. et al. · 2023

Full title: AF2BIND: Predicting ligand-binding sites using the pair representation of AlphaFold2

Authors: Gazizov, Artem; Lian, Anna; Goverde, Casper A.; Ovchinnikov, Sergey; Polizzi, Nicholas F.

DOI: https://doi.org/10.1101/2023.10.15.562410

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Structural Insights into Dopamine Receptor-Ligand Interactions: From Agonists to Antagonists

Barbosa, Emmanuel Duarte; Clift, Heather E.; Olson, Linda J. et al. · 2023

Full title: Structural Insights into Dopamine Receptor-Ligand Interactions: From Agonists to Antagonists

Authors: Barbosa, Emmanuel Duarte; Clift, Heather E.; Olson, Linda J.; Zhu, Lan; Liu, Wei

DOI: https://doi.org/10.1101/2023.11.03.565579

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Targeting transcription factors through an IMiD independent zinc finger domain

Liu, Bee Hui; Liu, Miao; Sridhar, R. et al. · 2024

Full title: Targeting transcription factors through an IMiD independent zinc finger domain

DOI: https://doi.org/10.1101/2024.01.03.574032

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NeuroFold: A Multimodal Approach to Generating Novel Protein Variants in silico

Amani, Keaun; Fish, Michael; Smith, Matthew D. et al. · 2024

Full title: NeuroFold: A Multimodal Approach to Generating Novel Protein Variants in silico

Authors: Amani, Keaun; Fish, Michael; Smith, Matthew D.; Castroverde, Christian Danve M.

DOI: https://doi.org/10.1101/2024.03.12.584504

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A Folding-Docking-Affinity framework for protein-ligand binding affinity prediction

Wu, Ming-Hsiu; Xie, Ziqian; Zhi, Degui · 2025

Full title: A Folding-Docking-Affinity framework for protein-ligand binding affinity prediction

Authors: Wu, Ming-Hsiu; Xie, Ziqian; Zhi, Degui

DOI: https://doi.org/10.1038/s42004-025-01506-1

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Complex-based Ligand-Binding Proteins Redesign by Equivariant Diffusion-based Generative Models

Nguyen, Viet Thanh Duy; Nguyen, Nhan Duc; Hy, Truong Son · 2024

Full title: Complex-based Ligand-Binding Proteins Redesign by Equivariant Diffusion-based Generative Models

Authors: Nguyen, Viet Thanh Duy; Nguyen, Nhan Duc; Hy, Truong Son

DOI: https://doi.org/10.1101/2024.04.17.589997

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Exploring Protein Patterns, Cavity Interactions, and Therapeutic Insights in Cancer

Nevado, Paloma Tejera; Otero-Carrasco, Belén; Rodríguez‐González, Alejandro · 2025

Full title: Exploring Protein Patterns, Cavity Interactions, and Therapeutic Insights in Cancer

Authors: Nevado, Paloma Tejera; Otero-Carrasco, Belén; Rodríguez‐González, Alejandro

DOI: https://doi.org/10.1101/2025.06.03.657615

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A potential implication of UDP-glucuronosyltransferase 2B10 in the detoxification of drugs used in pediatric hematopoietic stem cell transplantation setting: an in silico investigation

Robin, Shannon; Hassine, Khalil Ben; Muthukumaran, Jayaraman et al. · 2022

Full title: A potential implication of UDP-glucuronosyltransferase 2B10 in the detoxification of drugs used in pediatric hematopoietic stem cell transplantation setting: an in silico investigation

Authors: Robin, Shannon; Hassine, Khalil Ben; Muthukumaran, Jayaraman; Mlakar, Simona Jurković; Krajinović, Maja; Nava, Tiago; Uppugunduri, Chakradhara Rao S.; Ansari, Marc

DOI: https://doi.org/10.1186/s12860-021-00402-5

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Sequence-based drug-target affinity prediction using weighted graph neural networks

Jiang, Mingjian; Wang, Shuang; Zhang, Shugang et al. · 2022

Full title: Sequence-based drug-target affinity prediction using weighted graph neural networks

Authors: Jiang, Mingjian; Wang, Shuang; Zhang, Shugang; Zhou, Wei; Zhang, Yuanyuan; Li, Zhen

DOI: https://doi.org/10.1186/s12864-022-08648-9

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From byte to bench to bedside: molecular dynamics simulations and drug discovery

Ahmed, M.W.; Maldonado, Alex M.; Durrant, Jacob D. · 2023

Full title: From byte to bench to bedside: molecular dynamics simulations and drug discovery

Authors: Ahmed, M.W.; Maldonado, Alex M.; Durrant, Jacob D.

DOI: https://doi.org/10.1186/s12915-023-01791-z

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Molecular mechanism of interaction between fatty acid delta 6 desaturase and acyl-CoA by computational prediction

Cui, Jie; Chen, Haiqin; Tang, Xin et al. · 2022

Full title: Molecular mechanism of interaction between fatty acid delta 6 desaturase and acyl-CoA by computational prediction

Authors: Cui, Jie; Chen, Haiqin; Tang, Xin; Zhang, Hao; Chen, Yong Q.; Chen, Wei

DOI: https://doi.org/10.1186/s13568-022-01410-0

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Hypothetical protein CuvA (Rv1422) from Mycobacterium tuberculosis H37Rv interacts with uridine diphosphate N-acetylglucosamine as a key precursor of cell wall

Jeong, Yoon Chae; Park, Jihyun; Cheon, Yu Jeong et al. · 2023

Full title: Hypothetical protein CuvA (Rv1422) from Mycobacterium tuberculosis H37Rv interacts with uridine diphosphate N-acetylglucosamine as a key precursor of cell wall

Authors: Jeong, Yoon Chae; Park, Jihyun; Cheon, Yu Jeong; Lee, Ki Seog

DOI: https://doi.org/10.1186/s13765-023-00840-z

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A predicted structure of NADPH Oxidase 1 identifies key components of ROS generation and strategies for inhibition

Liu, Yezhou; Liang, Shiyu; Shi, Danfeng et al. · 2023

Full title: A predicted structure of NADPH Oxidase 1 identifies key components of ROS generation and strategies for inhibition

Authors: Liu, Yezhou; Liang, Shiyu; Shi, Danfeng; Zhang, Yue; Bai, Chen; Ye, Richard D.

DOI: https://doi.org/10.1371/journal.pone.0285206

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Towards a General Intermolecular Binding Affinity Calculator

Li, Wei · 2022

Full title: Towards a General Intermolecular Binding Affinity Calculator

Authors: Li, Wei

DOI: https://doi.org/10.20944/preprints202208.0213.v1

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A Folding-Docking-Affinity framework for protein-ligand binding affinity prediction

Wu, Ming-Hsiu; Xie, Ziqian; Zhi, Degui · 2025

Full title: A Folding-Docking-Affinity framework for protein-ligand binding affinity prediction

Authors: Wu, Ming-Hsiu; Xie, Ziqian; Zhi, Degui

DOI: https://doi.org/10.1038/s42004-025-01506-1

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AI based natural inhibitor targeting RPS20 for colorectal cancer treatment using integrated computational approaches

Nouman Ali; Roman Akbar; Amna Saleem et al. · 2025

Full title: AI based natural inhibitor targeting RPS20 for colorectal cancer treatment using integrated computational approaches

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DOI: https://doi.org/10.1038/s41598-025-07574-6

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Ren, Feng; Ding, Xiao; Zheng, Min et al. · 2023

Full title: AlphaFold accelerates artificial intelligence powered drug discovery: efficient discovery of a novel CDK20 small molecule inhibitor

DOI: https://doi.org/10.1039/d2sc05709c

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Full title: Exploring the selectivity of cytochrome P450 for enhanced novel anticancer agent synthesis

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DOI: https://doi.org/10.1039/d4fd00004h

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Full title: Generating 3D molecules conditional on receptor binding sites with deep generative models

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DOI: https://doi.org/10.1039/d1sc05976a

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Vaithyanathan, Prakash · 2021

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DOI: https://doi.org/10.1101/2021.10.15.464501

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DOI: https://doi.org/10.1101/2021.08.21.457196

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Full title: Flavobacterium johnsoniae Tyrosine Ammonia Lyase (FjTAL) in-silico Structure Prediction and Molecular Docking to L-Tyrosine, p-Coumaric Acid (pHCA) and Caffeic Acid

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Full title: Predicting the locations of cryptic pockets from single protein structures using the PocketMiner graph neural network

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Full title: Structural Modeling of Peptide Toxin - Ion Channel Interactions using RosettaDock

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DOI: https://doi.org/10.1101/2022.06.29.498146

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Full title: xTrimoDock: Rigid Protein Docking via Cross-Modal Representation Learning and Spectral Algorithm

Authors: Luo, Yujie; Li, Shaochuan; Sun, Yiwu; Wang, Ruijia; Tang, Tingting; Hongdu, Beiqi; Cheng, Xingyi; Shi, Chuan; Li, Hui; Song, Le

DOI: https://doi.org/10.1101/2023.02.06.527251

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Kolossváry, István; Sherman, Woody · 2023

Full title: Comprehensive Approach to Simulating Large Scale Conformational Changes in Biological Systems Utilizing a Path Collective Variable and New Barrier Restraint

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DOI: https://doi.org/10.1101/2023.03.26.534298

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Reconstruction of TrkB complex assemblies and localizing antidepressant targets using Artificial Intelligence

Xiang, Xufu; Qian, Chungen; Yao, Hanbo et al. · 2023

Full title: Reconstruction of TrkB complex assemblies and localizing antidepressant targets using Artificial Intelligence

Authors: Xiang, Xufu; Qian, Chungen; Yao, Hanbo; Li, Pengjie; Cheng, Bangning; Wei, Daoshun; An, Wenjun; Lu, Yuming; Chu, Ming; Wei, Lanlan; Liu, Bi‐Feng; Junfa, Xu; Liu, Xin; Xia, Fuzhen

DOI: https://doi.org/10.1101/2023.02.21.529454

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Fast, accurate ranking of engineered proteins by receptor binding propensity using structure modeling

Ding, Xiaozhe; Chen, Xinhong; Sullivan, Erin E. et al. · 2023

Full title: Fast, accurate ranking of engineered proteins by receptor binding propensity using structure modeling

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DOI: https://doi.org/10.1101/2023.01.11.523680

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Canner, Samuel W.; Shanker, Sudhanshu; Gray, Jeffrey J. · 2023

Full title: Structure-Based Neural Network Protein-Carbohydrate Interaction Predictions at the Residue Level

Authors: Canner, Samuel W.; Shanker, Sudhanshu; Gray, Jeffrey J.

DOI: https://doi.org/10.1101/2023.03.14.531382

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Hussain, Azam; Brooks, Charles L. · 2024

Full title: Guiding discovery of protein sequence-structure-function modeling

Authors: Hussain, Azam; Brooks, Charles L.

DOI: https://doi.org/10.1093/bioinformatics/btae002

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Understanding ATP binding to DosS catalytic domain with a short ATP-lid

Larson, Grant; Windsor, Peter; Smithwick, Elizabeth M. et al. · 2023

Full title: Understanding ATP binding to DosS catalytic domain with a short ATP-lid

Authors: Larson, Grant; Windsor, Peter; Smithwick, Elizabeth M.; Shi, Ke; Aihara, Hideki; Damodaran, Anoop R.; Bhagi‐Damodaran, Ambika

DOI: https://doi.org/10.1101/2023.05.29.542785

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McNaughton, Andrew; Shanklin, John; Raugei, Simone et al. · 2023

Full title: Data-Driven Modeling and Analysis of Fatty Acid Desaturase in Plants

Authors: McNaughton, Andrew; Shanklin, John; Raugei, Simone; Kumar, Neeraj

DOI: https://doi.org/10.1101/2023.08.17.553759

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HTLV-1 reverse transcriptase homology model provides structural basis for sensitivity to existing nucleoside/nucleotide reverse transcriptase inhibitors

Tardiota, Nicolas; Jaberolansar, Noushin; Lackenby, Julia et al. · 2023

Full title: HTLV-1 reverse transcriptase homology model provides structural basis for sensitivity to existing nucleoside/nucleotide reverse transcriptase inhibitors

Authors: Tardiota, Nicolas; Jaberolansar, Noushin; Lackenby, Julia; Chappell, Keith J.; O’Donnell, Jake S.

DOI: https://doi.org/10.1101/2023.05.25.542289

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Finke, Felicitas; Hungerland, Jonathan; Solov'yov, Ilia A et al. · 2025

Full title: Different receptor models show differences in ligand binding strength and location: a computational drug screening for the tick-borne encephalitis virus.

Authors: Finke, Felicitas; Hungerland, Jonathan; Solov'yov, Ilia A; Schuhmann, Fabian

DOI: https://doi.org/10.1007/s11030-024-10850-8

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Ins and outs of AlphaFold2 transmembrane protein structure predictions

Hegedűs, Tamás; Geisler, Markus; Lukács, Gergely L. et al. · 2022

Full title: Ins and outs of AlphaFold2 transmembrane protein structure predictions

Authors: Hegedűs, Tamás; Geisler, Markus; Lukács, Gergely L.; Farkas, Bianka

DOI: https://doi.org/10.1007/s00018-021-04112-1

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Modelling peptide–protein complexes: docking, simulations and machine learning

Mondal, Arup; Chang, Liwei; Pérez, Alberto · 2022

Full title: Modelling peptide–protein complexes: docking, simulations and machine learning

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DOI: https://doi.org/10.1017/qrd.2022.14

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Full title: Review: Modeling peptide-protein complexes: docking, simulations and machine learning — R0/PR2

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DOI: https://doi.org/10.1017/qrd.2022.14.pr2

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Full title: Crystal structure of steroid reductase SRD5A reveals conserved steroid reduction mechanism

DOI: https://doi.org/10.1038/s41467-020-20675-2

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Full title: Structural basis for receptor selectivity and inverse agonism in S1P5 receptors

DOI: https://doi.org/10.1038/s41467-022-32447-1

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Full title: Predicting locations of cryptic pockets from single protein structures using the PocketMiner graph neural network

Authors: Meller, Artur; Ward, Michael D.; Borowsky, Jonathan; Kshirsagar, Meghana; Lotthammer, Jeffrey M.; Oviedo, Felipe; Ferres, Juan Lavista; Bowman, Gregory R.

DOI: https://doi.org/10.1038/s41467-023-36699-3

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Full title: Biosensor and machine learning-aided engineering of an amaryllidaceae enzyme

DOI: https://doi.org/10.1038/s41467-024-46356-y

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Ragavan, Vinitha N.; Nair, Pramod C.; Jarzebska, Natalia et al. · 2023

Full title: A multicentric consortium study demonstrates that dimethylarginine dimethylaminohydrolase 2 is not a dimethylarginine dimethylaminohydrolase

DOI: https://doi.org/10.1038/s41467-023-38467-9

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Full title: Theoretical studies on RNA recognition by Musashi 1 RNA-binding protein

Authors: Darai, Nitchakan; Mahalapbutr, Panupong; Wolschann, Peter; Lee, Vannajan Sanghiran; Wolfinger, Michael T.; Rungrotmongkol, Thanyada

DOI: https://doi.org/10.1038/s41598-022-16252-w

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Abrahams-October, Zainonesa; Johnson, Rabia; Benjeddou, Mongi et al. · 2022

Full title: The determination of the effect(s) of solute carrier family 22-member 2 (SLC22A2) haplotype variants on drug binding via molecular dynamic simulation systems

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DOI: https://doi.org/10.1038/s41598-022-21291-4

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Theoretical studies of arbutin, glutathione, and sea cucumber extracts as inhibitors of tyrosinase.

Zheng, Zheng; Zhang, Shizhuo; Jiang, Tao et al. · 2025

Full title: Theoretical studies of arbutin, glutathione, and sea cucumber extracts as inhibitors of tyrosinase.

Authors: Zheng, Zheng; Zhang, Shizhuo; Jiang, Tao; Liu, Wenlang; Xu, Zifan; Shen, Xinyi; Sun, Tiantian

DOI: https://doi.org/10.1038/s41598-025-06316-y

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Bertoline, Letícia M. F.; Lima, Angélica N.; Krieger, José Eduardo et al. · 2023

Full title: Before and after AlphaFold2: An overview of protein structure prediction

Authors: Bertoline, Letícia M. F.; Lima, Angélica N.; Krieger, José Eduardo; Teixeira, Samantha K.

DOI: https://doi.org/10.3389/fbinf.2023.1120370

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Kumar, Rakesh; Ningombam, Somorjit Singh; Kumar, Rahul et al. · 2022

Full title: Comprehensive mutations analyses of FTO (fat mass and obesity-associated gene) and their effects on FTO’s substrate binding implicated in obesity

Authors: Kumar, Rakesh; Ningombam, Somorjit Singh; Kumar, Rahul; Goel, Harsh; Gogia, Ajay; Khurana, Sachin; Deo, S. V. S.; Mathur, Sandeep; Tanwar, Pranay

DOI: https://doi.org/10.3389/fnut.2022.852944

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Full title: A cheminformatics and network pharmacology approach to elucidate the mechanism of action of Mycobacterium tuberculosis γ-carbonic anhydrase inhibitors

Authors: A. Manaithiya; R. Bhowmik; Kunal Bhattacharya; Rajarshi Ray; S. S. Shyamal; F. Carta; C. Supuran; Seppo Parkkila; A. Aspatwar

DOI: https://doi.org/10.3389/fphar.2024.1457012

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Artificial Intelligence: A New Tool for Structure-Based G Protein-Coupled Receptor Drug Discovery.

Chung, Jason; Hahn, Hyunggu; Flores-Espinoza, Emmanuel et al. · 2025

Full title: Artificial Intelligence: A New Tool for Structure-Based G Protein-Coupled Receptor Drug Discovery.

Authors: Chung, Jason; Hahn, Hyunggu; Flores-Espinoza, Emmanuel; Thomsen, Alex R B

DOI: https://doi.org/10.3390/biom15030423

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Structural Characterization and Molecular Dynamics Study of the REPI Fusion Protein from Papaver somniferum L.

Diaz-Bárcena, Alba; Pacios, Luis F.; Giraldo, Patricia · 2023

Full title: Structural Characterization and Molecular Dynamics Study of the REPI Fusion Protein from Papaver somniferum L.

Authors: Diaz-Bárcena, Alba; Pacios, Luis F.; Giraldo, Patricia

DOI: https://doi.org/10.3390/biom14010002

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Insight into the Mode of Action of 8-Hydroxyquinoline-Based Blockers on the Histamine Receptor 2

Patel, Amisha; Marquez-Gomez, Paola L.; Torp, Lily R. et al. · 2023

Full title: Insight into the Mode of Action of 8-Hydroxyquinoline-Based Blockers on the Histamine Receptor 2

Authors: Patel, Amisha; Marquez-Gomez, Paola L.; Torp, Lily R.; Gao, Lily; Peralta‐Yahya, Pamela

DOI: https://doi.org/10.3390/bios13060571

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Advances in Computational Intelligence-Based Methods of Structure and Function Prediction of Proteins

Zhang, Jian; Qian, Jingjing · 2024

Full title: Advances in Computational Intelligence-Based Methods of Structure and Function Prediction of Proteins

Authors: Zhang, Jian; Qian, Jingjing

DOI: https://doi.org/10.3390/biom14091083

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Exploring Quercetin Hydrate’s Potential as an Antiviral Treatment for Oropouche Virus

Menezes, Gabriela de Lima; Saivish, Marielena Vogel; Sacchetto, Lívia et al. · 2023

Full title: Exploring Quercetin Hydrate’s Potential as an Antiviral Treatment for Oropouche Virus

DOI: https://doi.org/10.3390/biophysica3030032

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Limitations of Protein Structure Prediction Algorithms in Therapeutic Protein Development

Niazi, Sarfaraz K.; Mariam, Zamara; Paracha, Rehan Zafar · 2024

Full title: Limitations of Protein Structure Prediction Algorithms in Therapeutic Protein Development

Authors: Niazi, Sarfaraz K.; Mariam, Zamara; Paracha, Rehan Zafar

DOI: https://doi.org/10.3390/biomedinformatics4010007

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Theoretical Studies of Cyanophycin Dipeptides as Inhibitors of Tyrosinases

Krzemińska, Agnieszka; Kwiatos, Natalia; Soares, Franciela Arenhart et al. · 2022

Full title: Theoretical Studies of Cyanophycin Dipeptides as Inhibitors of Tyrosinases

Authors: Krzemińska, Agnieszka; Kwiatos, Natalia; Soares, Franciela Arenhart; Steinbüchel, Alexander

DOI: https://doi.org/10.3390/ijms23063335

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The Giardial Arginine Deiminase Participates in Giardia-Host Immunomodulation in a Structure-Dependent Fashion via Toll-like Receptors

Fernández‐Lainez, Cynthia; Ji, De; Enríquez‐Flores, Sergio et al. · 2022

Full title: The Giardial Arginine Deiminase Participates in Giardia-Host Immunomodulation in a Structure-Dependent Fashion via Toll-like Receptors

DOI: https://doi.org/10.3390/ijms231911552

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Computational Study of Molecular Mechanism for the Involvement of Human Serum Albumin in the Renin-Angiotensin-Aldosterone System.

Belinskaia, Daria A; Shestakova, Natalia N; Samodurova, Kamila V et al. · 2024

Full title: Computational Study of Molecular Mechanism for the Involvement of Human Serum Albumin in the Renin-Angiotensin-Aldosterone System.

Authors: Belinskaia, Daria A; Shestakova, Natalia N; Samodurova, Kamila V; Goncharov, Nikolay V

DOI: https://doi.org/10.3390/ijms251910260

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Modeling and Analysis of HIV-1 Pol Polyprotein as a Case Study for Predicting Large Polyprotein Structures

Hao, Ming; Imamichi, Tomozumi; Chang, Weizhong · 2024

Full title: Modeling and Analysis of HIV-1 Pol Polyprotein as a Case Study for Predicting Large Polyprotein Structures

Authors: Hao, Ming; Imamichi, Tomozumi; Chang, Weizhong

DOI: https://doi.org/10.3390/ijms25031809

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iBio-GATS—A Semi-Automated Workflow for Structural Modelling of Insect Odorant Receptors

Thanu, Vaanathi Chidambara; Jabeen, Amara; Ranganathan, Shoba · 2024

Full title: iBio-GATS—A Semi-Automated Workflow for Structural Modelling of Insect Odorant Receptors

Authors: Thanu, Vaanathi Chidambara; Jabeen, Amara; Ranganathan, Shoba

DOI: https://doi.org/10.3390/ijms25053055

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Evaluation of AI-Predicted GH11 Xylanase Models Against a Previously Unreported Experimental Structure: Implications for Conformational Accuracy and Ligand Binding.

Nam, Ki Hyun · 2026

Full title: Evaluation of AI-Predicted GH11 Xylanase Models Against a Previously Unreported Experimental Structure: Implications for Conformational Accuracy and Ligand Binding.

Authors: Nam, Ki Hyun

DOI: https://doi.org/10.3390/ijms27031370

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Potential Compounds in Indonesian Herbal Plants using Computational Screening for Inhibitory Activity Against Chikungunya Virus Envelope Protein E2

Inda Setyawati; Fatma Ayyalla; Fadhilla Ilyas et al. · 2024

Full title: Potential Compounds in Indonesian Herbal Plants using Computational Screening for Inhibitory Activity Against Chikungunya Virus Envelope Protein E2

Authors: Inda Setyawati; Fatma Ayyalla; Fadhilla Ilyas; Mikael Kristiadi; Aprijal Ghiyas; Setiawan

DOI: https://doi.org/10.36378/juatika.v6i2.3616

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FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction

Alex Morehead; Jianlin Cheng · 2024

Full title: FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction

Authors: Alex Morehead; Jianlin Cheng

DOI: https://doi.org/10.48550/arxiv.2412.10966

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Structural and Functional Studies of Proteins Involved in the Regulation of Fatty Acid Metabolism

Zelencova-Gopejenko, Diāna; Zelencova-Gopejenko, Diāna · 2023

Full title: Structural and Functional Studies of Proteins Involved in the Regulation of Fatty Acid Metabolism

Authors: Zelencova-Gopejenko, Diāna; Zelencova-Gopejenko, Diāna

DOI: https://doi.org/10.7250/9789934229121

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Harnessing AlphaFold to reveal hERG channel conformational state secrets

Ngo, Khoa; Yang, Pei‐Chi; Yarov‐Yarovoy, Vladimir et al. · 2024

Full title: Harnessing AlphaFold to reveal hERG channel conformational state secrets

Authors: Ngo, Khoa; Yang, Pei‐Chi; Yarov‐Yarovoy, Vladimir; Clancy, Colleen E.; Vorobyov, Igor

DOI: https://doi.org/10.1101/2024.01.27.577468

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How Banf1 Functions to Inhibit the Activity of PARP1

Bai, Bond; Bai, Bond · 2024

Full title: How Banf1 Functions to Inhibit the Activity of PARP1

Authors: Bai, Bond; Bai, Bond

DOI: https://doi.org/10.5204/thesis.eprints.254811

Paper

MOLECULAR INSIGHTS INTO BINDING BEHAVIOUR OF LAMOTRIGINE WITH INITIATION FACTOR 2 PROTEIN: AN INTEGRATED COMPUTATIONAL STUDIES

Arora, Smriti; Patra, Jeevan · 2022

Full title: MOLECULAR INSIGHTS INTO BINDING BEHAVIOUR OF LAMOTRIGINE WITH INITIATION FACTOR 2 PROTEIN: AN INTEGRATED COMPUTATIONAL STUDIES

Authors: Arora, Smriti; Patra, Jeevan

DOI: https://doi.org/10.1101/2022.08.26.505506

Thesis

An overview of data-driven HADDOCK strategies in CAPRI rounds 38-45

Koukos, Panagiotis I.; Roel-Touris, Jorge; Ambrosetti, Francesco et al. · 2020

Full title: An overview of data-driven HADDOCK strategies in CAPRI rounds 38-45

DOI: https://dspace.library.uu.nl/handle/1874/390638

Thesis

Development of Computer Aided Drug Design Algorithms and Application to be APOBEC3 Family of Proteins

Wagner, Jeffrey Robert Rothfeld · 2018

Full title: Development of Computer Aided Drug Design Algorithms and Application to be APOBEC3 Family of Proteins

Authors: Wagner, Jeffrey Robert Rothfeld

DOI: https://escholarship.org/uc/item/9c66d756

Thesis

New approaches to accelerate structure-based small molecule discovery

Flynn, Alex James · 2023

Full title: New approaches to accelerate structure-based small molecule discovery

Authors: Flynn, Alex James

DOI: https://etheses.whiterose.ac.uk/id/eprint/34242/1/AF%20corrected%20thesis%20for%20upload.pdf

Thesis

Deep learning approaches for conformational flexibility and switching properties in protein design

Rudden, Lucas S. P.; Hijazi, Mahdi; Barth, Patrick · 2022

Full title: Deep learning approaches for conformational flexibility and switching properties in protein design

Authors: Rudden, Lucas S. P.; Hijazi, Mahdi; Barth, Patrick

DOI: https://infoscience.epfl.ch/handle/20.500.14299/190456

Thesis

Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures

Kwon, S; Safer, J; Nguyen, DT et al. · 2025

Full title: Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures

Authors: Kwon, S; Safer, J; Nguyen, DT; Hoksza, D; May, P; Arbesfeld, JA; Rubin, AF; Campbell, AJ; Burgin, A; Iqbal, S

DOI: https://hdl.handle.net/11343/358701

Thesis

Machine Learning for Kinase Drug Discovery

Kimber, Talia Beatrice · 2023

Full title: Machine Learning for Kinase Drug Discovery

Authors: Kimber, Talia Beatrice

DOI: https://refubium.fu-berlin.de/handle/fub188/38039

Thesis

Defining the limits of homology modeling in information-driven protein docking

Garcia Lopes Maia Rodrigues, João; Melquiond, A S J; Karaca, E et al. · 2013

Full title: Defining the limits of homology modeling in information-driven protein docking

DOI: https://dspace.library.uu.nl/handle/1874/290387

Thesis

Next challenges in protein–protein docking: from proteome to interactome and beyond

Melquiond, A.S.J.; Karaca, E.; Kastritis, P. et al. · 2012

Full title: Next challenges in protein–protein docking: from proteome to interactome and beyond

Authors: Melquiond, A.S.J.; Karaca, E.; Kastritis, P.; Bonvin, A.M.J.J.

DOI: https://dspace.library.uu.nl/handle/1874/255698

Thesis

Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2

Vreven, Thom; Moal, Iain H.; Vangone, Anna et al. · 2015

Full title: Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2

DOI: https://dspace.library.uu.nl/handle/1874/354214

Thesis

A benchmark testing ground for integrating homology modeling and protein docking

Bohnuud, Tanggis; Luo, Lingqi; Wodak, Shoshana J et al. · 2017

Full title: A benchmark testing ground for integrating homology modeling and protein docking

Authors: Bohnuud, Tanggis; Luo, Lingqi; Wodak, Shoshana J; Bonvin, Alexandre M J J; Weng, Zhiping; Vajda, Sandor; Schueler-Furman, Ora; Kozakov, Dima

DOI: https://dspace.library.uu.nl/handle/1874/344418

Thesis

Membrane proteins structures: A review on computational modeling tools

Almeida, Jose G; Preto, Antonio J.; Koukos, Panos et al. · 2017

Full title: Membrane proteins structures: A review on computational modeling tools

Authors: Almeida, Jose G; Preto, Antonio J.; Koukos, Panos; Bonvin, Alexandre M.J.J.; de Sousa Moreira, Irina

DOI: https://dspace.library.uu.nl/handle/1874/363472

Thesis

Folding Then Binding vs Folding Through Binding in Macrocyclic Peptide Inhibitors of Human Pancreatic α-Amylase

Goldbach, Leander; Vermeulen, Bram J A; Caner, Sami et al. · 2019

Full title: Folding Then Binding vs Folding Through Binding in Macrocyclic Peptide Inhibitors of Human Pancreatic α-Amylase

DOI: https://dspace.library.uu.nl/handle/1874/384217

Thesis

Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape

Basciu, Andrea; Malloci, Giuliano; Pietrucci, Fabio et al. · 2019

Full title: Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape

Authors: Basciu, Andrea; Malloci, Giuliano; Pietrucci, Fabio; Bonvin, Alexandre M.J.J.; Vargiu, Attilio V.

DOI: https://dspace.library.uu.nl/handle/1874/387042

Thesis

Pre- and post-docking sampling of conformational changes using ClustENM and HADDOCK for protein-protein and protein-DNA systems

Kurkcuoglu, Zeynep; Bonvin, Alexandre M.J.J. · 2020

Full title: Pre- and post-docking sampling of conformational changes using ClustENM and HADDOCK for protein-protein and protein-DNA systems

Authors: Kurkcuoglu, Zeynep; Bonvin, Alexandre M.J.J.

DOI: https://dspace.library.uu.nl/handle/1874/391763

Thesis

Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4

Basciu, Andrea; Koukos, Panagiotis I; Malloci, Giuliano et al. · 2020

Full title: Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4

Authors: Basciu, Andrea; Koukos, Panagiotis I; Malloci, Giuliano; Bonvin, Alexandre M J J; Vargiu, Attilio V

DOI: https://dspace.library.uu.nl/handle/1874/391767

Thesis

Impact of AlphaFold on Structure Prediction of Protein Complexes: The CASP15-CAPRI Experiment

Lensink, Marc; Brysbaert, Guillaume; Raouraoua, Nessim et al. · 2023

Full title: Impact of AlphaFold on Structure Prediction of Protein Complexes: The CASP15-CAPRI Experiment

DOI: https://dspace.library.uu.nl/handle/1874/438081

Thesis

DeepRank-GNN: A Graph Neural Network Framework to Learn Patterns in Protein-Protein Interfaces

Réau, Manon; Renaud, Nicolas; Xue, Li C et al. · 2023

Full title: DeepRank-GNN: A Graph Neural Network Framework to Learn Patterns in Protein-Protein Interfaces

Authors: Réau, Manon; Renaud, Nicolas; Xue, Li C; Bonvin, Alexandre M J J

DOI: https://dspace.library.uu.nl/handle/1874/425720

Thesis

Improving the quality of co-evolution intermolecular contact prediction with DisVis

van Keulen, Siri C.; Bonvin, Alexandre M.J.J. · 2023

Full title: Improving the quality of co-evolution intermolecular contact prediction with DisVis

Authors: van Keulen, Siri C.; Bonvin, Alexandre M.J.J.

DOI: https://dspace.library.uu.nl/handle/1874/434156

Thesis

Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study

Schweke, Hugo; Xu, Qifang; Tauriello, Gerardo et al. · 2023

Full title: Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study

DOI: https://dspace.library.uu.nl/handle/1874/434203

Thesis

MetaScore: A Novel Machine-Learning-Based Approach to Improve Traditional Scoring Functions for Scoring Protein-Protein Docking Conformations

Jung, Yong; Geng, Cunliang; Bonvin, Alexandre M. J. J. et al. · 2023

Full title: MetaScore: A Novel Machine-Learning-Based Approach to Improve Traditional Scoring Functions for Scoring Protein-Protein Docking Conformations

Authors: Jung, Yong; Geng, Cunliang; Bonvin, Alexandre M. J. J.; Xue, Li C.; Honavar, Vasant G.

DOI: https://dspace.library.uu.nl/handle/1874/436107

Thesis

Casting Protein Structure Predictors as Energy-Based Models for Binder Design and Scoring

Nori, Divya · 2025

Full title: Casting Protein Structure Predictors as Energy-Based Models for Binder Design and Scoring

Authors: Nori, Divya

DOI: https://hdl.handle.net/1721.1/162975

Thesis

Comparing Native Crystal Structures and AlphaFold2 Predicted Water-Soluble G Protein-Coupled Receptor QTY Variants

Skuhersky, Michael A.; Tao, Fei; Qing, Rui et al. · 2021

Full title: Comparing Native Crystal Structures and AlphaFold2 Predicted Water-Soluble G Protein-Coupled Receptor QTY Variants

Authors: Skuhersky, Michael A.; Tao, Fei; Qing, Rui; Smorodina, Eva; Jin, David; Zhang, Shuguang

DOI: https://hdl.handle.net/1721.1/138236

Thesis

Inference Time Search for Protein Structure Prediction

Qi, Richard · 2025

Full title: Inference Time Search for Protein Structure Prediction

Authors: Qi, Richard

DOI: https://hdl.handle.net/1721.1/162989

Thesis

Structure Prediction and Virtual Screening: Application to G Protein-coupled Receptors

Marko, Adam Christian · 2009

Full title: Structure Prediction and Virtual Screening: Application to G Protein-coupled Receptors

Authors: Marko, Adam Christian

DOI: https://escholarship.org/uc/item/1cz1433r

Thesis

Determination of X-ray Crystal Structure of Human E3 Ligase in Complex with Small Molecule Ligands

Huang, Shih-Ting · 2022

Full title: Determination of X-ray Crystal Structure of Human E3 Ligase in Complex with Small Molecule Ligands

Authors: Huang, Shih-Ting

DOI: https://escholarship.org/uc/item/1ss6x4k0

Thesis

The Nobel Prize in Chemistry: past, present, and future of AI in biology

Abriata, Luciano A. · 2025

Full title: The Nobel Prize in Chemistry: past, present, and future of AI in biology

Authors: Abriata, Luciano A.

DOI: https://infoscience.epfl.ch/handle/20.500.14299/245542

Thesis

One-shot Design of Functional Protein Binders with Bindcraft

Pacesa, Martin; Nickel, Lennart; Schellhaas, Christian et al. · 2025

Full title: One-shot Design of Functional Protein Binders with Bindcraft

DOI: https://infoscience.epfl.ch/handle/20.500.14299/253809

Thesis

Computational modeling of the olfactory receptor Olfr73 suggests a molecular basis for low potency of olfactory receptor-activating compounds

Yuan, Shuguang; Dahoun, Thamani; Brugarolas, Marc et al. · 2019

Full title: Computational modeling of the olfactory receptor Olfr73 suggests a molecular basis for low potency of olfactory receptor-activating compounds

Authors: Yuan, Shuguang; Dahoun, Thamani; Brugarolas, Marc; Pick, Horst; Filipek, Slawomir; Vogel, Horst

DOI: https://infoscience.epfl.ch/handle/20.500.14299/157572

Thesis

Expanding the boundaries of ligand-target modeling by exascale calculations

Bolnykh, Viacheslav; Rossetti, Giulia; Rothlisberger, Ursula et al. · 2021

Full title: Expanding the boundaries of ligand-target modeling by exascale calculations

Authors: Bolnykh, Viacheslav; Rossetti, Giulia; Rothlisberger, Ursula; Carloni, Paolo

DOI: https://infoscience.epfl.ch/handle/20.500.14299/178275

Thesis

COMPUTATIONAL TECHNIQUES TO EVALUATE AT ATOMIC LEVEL THE MECHANISM OF MOLECULAR BINDING

C. Paissoni · 2017

Full title: COMPUTATIONAL TECHNIQUES TO EVALUATE AT ATOMIC LEVEL THE MECHANISM OF MOLECULAR BINDING

Authors: C. Paissoni

DOI: http://hdl.handle.net/2434/480031

Thesis

Protein Structure Accuracy Prediction with Deep Learning and its Application to Structure Prediction and Design

Hiranuma, Naozumi · 2022

Full title: Protein Structure Accuracy Prediction with Deep Learning and its Application to Structure Prediction and Design

Authors: Hiranuma, Naozumi

DOI: http://hdl.handle.net/1773/48478

Thesis

Developing a high throughput in silico screening pipeline for the discovery of novel antifungals

Hambly, Jacob · 2025

Full title: Developing a high throughput in silico screening pipeline for the discovery of novel antifungals

Authors: Hambly, Jacob

DOI: https://hdl.handle.net/10214/29207

Thesis

How proteins get in touch: Interface prediction and docking of protein complexes

de Vries, S.J. · 2009

Full title: How proteins get in touch: Interface prediction and docking of protein complexes

Authors: de Vries, S.J.

DOI: https://dspace.library.uu.nl/handle/1874/33805

Thesis

Modelling protein-DNA interactions: bend and twist until it fits

van Dijk, M. · 2010

Full title: Modelling protein-DNA interactions: bend and twist until it fits

Authors: van Dijk, M.

DOI: https://dspace.library.uu.nl/handle/1874/40020

Thesis

Computational methods for the structure-based design of protein-binding peptides

Swanson, Sebastian Robles · 2023

Full title: Computational methods for the structure-based design of protein-binding peptides

Authors: Swanson, Sebastian Robles

DOI: https://hdl.handle.net/1721.1/153028

Thesis

Biomolecular Modeling at Scale

Wohlwend, Jeremy · 2025

Full title: Biomolecular Modeling at Scale

Authors: Wohlwend, Jeremy

DOI: https://hdl.handle.net/1721.1/164122

Thesis

Modeling Biomolecular Interactions with Generative Models

Corso, Gabriele · 2025

Full title: Modeling Biomolecular Interactions with Generative Models

Authors: Corso, Gabriele

DOI: https://hdl.handle.net/1721.1/164058

Thesis

Integrating conformational and protonation equilibria in biomolecular modeling

Kim, Meekyum Olivia · 2015

Full title: Integrating conformational and protonation equilibria in biomolecular modeling

Authors: Kim, Meekyum Olivia

DOI: https://escholarship.org/uc/item/0rp5481g

Thesis

Physics-based Refinement of Proteins in Model Systems

Sellers, Benjamin D · 2008

Full title: Physics-based Refinement of Proteins in Model Systems

Authors: Sellers, Benjamin D

DOI: https://escholarship.org/uc/item/1tv93190

Thesis

Ligand Desolvation in Molecular Docking (How, Why, and With What?)

Mysinger, Michael McLeod · 2012

Full title: Ligand Desolvation in Molecular Docking (How, Why, and With What?)

Authors: Mysinger, Michael McLeod

DOI: https://escholarship.org/uc/item/24t6017j

Thesis

Improved prediction of structurally diverse de novo proteins

Orr, Benjamin David · 2025

Full title: Improved prediction of structurally diverse de novo proteins

Authors: Orr, Benjamin David

DOI: https://escholarship.org/uc/item/6r869912

Thesis

Computational biochemical approaches to protein structure prediction and drug discovery

Biehn, Sarah Elizabeth · 2022

Full title: Computational biochemical approaches to protein structure prediction and drug discovery

Authors: Biehn, Sarah Elizabeth

DOI: http://rave.ohiolink.edu/etdc/view?acc_num=osu1649673976879668

Thesis

Advancing Computational Protein Modeling: Sparse Data Integration in Rosetta and AlphaFold2

Drake, Zachary Colton · 2025

Full title: Advancing Computational Protein Modeling: Sparse Data Integration in Rosetta and AlphaFold2

Authors: Drake, Zachary Colton

DOI: http://rave.ohiolink.edu/etdc/view?acc_num=osu1752424969978784

Thesis

Structural and pharmacological analysis of novel adenosine A2A receptor ligands to guide rational drug design

Zilian, Claudia Tania · 2022

Full title: Structural and pharmacological analysis of novel adenosine A2A receptor ligands to guide rational drug design

Authors: Zilian, Claudia Tania

DOI: https://etheses.whiterose.ac.uk/id/eprint/30804/1/Zilian_CT_Biomedical-Sciences_PhD_2022.pdf

Thesis

Discrete approaches for leveraging g protein-coupled receptors as therapeutic tools

Marcus Saarinen (18666955) · 2024

Full title: Discrete approaches for leveraging g protein-coupled receptors as therapeutic tools

Authors: Marcus Saarinen (18666955)

DOI: oai:figshare.com:article/27055156

Thesis

Insights on Protein Conformational Diversity at the Ligand Binding Site Level

Feidakis, Christos · 2025

Full title: Insights on Protein Conformational Diversity at the Ligand Binding Site Level

Authors: Feidakis, Christos

DOI: http://hdl.handle.net/20.500.11956/196368

Thesis

Generative Modeling of Full-Atom Protein Conformations using Latent Diffusion on Graph Embeddings

Sengar, Aditya; Hariri, Ali; Probst, Daniel et al. · 2025

Full title: Generative Modeling of Full-Atom Protein Conformations using Latent Diffusion on Graph Embeddings

Authors: Sengar, Aditya; Hariri, Ali; Probst, Daniel; Barth, Patrick; Vandergheynst, Pierre

DOI: https://infoscience.epfl.ch/handle/20.500.14299/251548

Thesis

A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer

Krapp, Lucien Fabrice · 2023

Full title: A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer

Authors: Krapp, Lucien Fabrice

DOI: https://infoscience.epfl.ch/handle/20.500.14299/201949

Thesis

Protein target highlights in CASP15: Analysis of models by structure providers

Alexander, Leila T.; Durairaj, Janani; Kryshtafovych, Andriy et al. · 2023

Full title: Protein target highlights in CASP15: Analysis of models by structure providers

DOI: https://infoscience.epfl.ch/handle/20.500.14299/199869

Thesis

Computational modeling, prediction, and design of Protein-Protein interactions

Harmalkar, Ameya Uddhav · 2023

Full title: Computational modeling, prediction, and design of Protein-Protein interactions

Authors: Harmalkar, Ameya Uddhav

DOI: http://jhir.library.jhu.edu/handle/1774.2/68944

Thesis

Predicting protein interactions using geometric deep learning on protein surfaces

Sverrisson, Freyr · 2024

Full title: Predicting protein interactions using geometric deep learning on protein surfaces

Authors: Sverrisson, Freyr

DOI: https://infoscience.epfl.ch/handle/20.500.14299/206239

Thesis

Protein Target Highlights in CASP16 : Insights From the Structure Providers

None · 2025

Full title: Protein Target Highlights in CASP16 : Insights From the Structure Providers

Authors: None

DOI: https://hdl.handle.net/11343/362434

Thesis

The new insights into protein structures by computational methods

Zou, Ye · 2022

Full title: The new insights into protein structures by computational methods

Authors: Zou, Ye

DOI: https://hdl.handle.net/2097/42225

Thesis

The application of advanced structural bioinformatics methods to parasitic membrane proteins

Murphy, David · 2024

Full title: The application of advanced structural bioinformatics methods to parasitic membrane proteins

Authors: Murphy, David

DOI: https://livrepository.liverpool.ac.uk/3182410/1/201365014_Jun2024.pdf

Thesis

Interdisciplinary techniques in protein binding prediction and crystal engineering

DeRoo, Jacob Benjamin, author; Reynolds, Melissa, advisor; Snow, Christopher D., advisor et al. · 2024

Full title: Interdisciplinary techniques in protein binding prediction and crystal engineering

Authors: DeRoo, Jacob Benjamin, author; Reynolds, Melissa, advisor; Snow, Christopher D., advisor; Reardon, Ken, committee member; Zabel, Mark, committee member

DOI: https://hdl.handle.net/10217/239831

Thesis

Structural Analysis of 20S Proteasome and Development of Structure-Based Virtual Screening Methods

Arciniega Castro, Marcelino · 2014

Full title: Structural Analysis of 20S Proteasome and Development of Structure-Based Virtual Screening Methods

Authors: Arciniega Castro, Marcelino

DOI: https://mediatum.ub.tum.de/1221441

Thesis

Impact of Protein conformational Changes on Molecular Docking - Design of a Docking Approach including Receptor Flexibility

Leis, Simon · 2013

Full title: Impact of Protein conformational Changes on Molecular Docking - Design of a Docking Approach including Receptor Flexibility

Authors: Leis, Simon

DOI: https://mediatum.ub.tum.de/1115345

Thesis

Quality assessment of docked protein interfaces using 3D convolution

Bontha, Mridula, author; Ben-Hur, Asa, advisor; Beveridge, J. Ross, committee member et al. · 2021

Full title: Quality assessment of docked protein interfaces using 3D convolution

Authors: Bontha, Mridula, author; Ben-Hur, Asa, advisor; Beveridge, J. Ross, committee member; King, Emily J., committee member

DOI: https://hdl.handle.net/10217/232476

Thesis

Deep Learning Tools for Protein Binder Design

Bennett, Nathaniel · 2023

Full title: Deep Learning Tools for Protein Binder Design

Authors: Bennett, Nathaniel

DOI: http://hdl.handle.net/1773/50187

Thesis

Enhancing Protein Sequence Design through Augmented Machine Learning of Hydrogen Bonding Networks

Tan, Kevin · 2024

Full title: Enhancing Protein Sequence Design through Augmented Machine Learning of Hydrogen Bonding Networks

Authors: Tan, Kevin

DOI: https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37379285

Thesis

CSM-Potential: mapping protein interactions and biological ligands in 3D space using geometric deep learning

Rodrigues, CHM; Ascher, DB · 2022

Full title: CSM-Potential: mapping protein interactions and biological ligands in 3D space using geometric deep learning

Authors: Rodrigues, CHM; Ascher, DB

DOI: https://hdl.handle.net/11343/316133

Thesis

Optimization of protein-protein docking for predicting Fc-protein interactions

Agostino, M; Mancera, RL; Ramsland, PA et al. · 2021

Full title: Optimization of protein-protein docking for predicting Fc-protein interactions

Authors: Agostino, M; Mancera, RL; Ramsland, PA; Fernández-Recio, J

DOI: https://hdl.handle.net/11343/291528

Thesis

Structure-Based Discovery of Lipoteichoic Acid Synthase Inhibitors

Wezen, Xavier Chee; Chandran, Aneesh; Eapen, Rohan Sakariah et al. · 2022

Full title: Structure-Based Discovery of Lipoteichoic Acid Synthase Inhibitors

DOI: https://livrepository.liverpool.ac.uk/3158905/1/Structure-Based%20Discovery%20of%20Lipoteichoic%20Acid%20Synthase%20Inhibitors.pdf

Thesis

Using Molecular Dynamics and Enhanced Sampling to Predict Binding Poses Beyond The Rigid-Docking Approximation

Åberg, Emil · 2017

Full title: Using Molecular Dynamics and Enhanced Sampling to Predict Binding Poses Beyond The Rigid-Docking Approximation

Authors: Åberg, Emil

DOI: http://lup.lub.lu.se/student-papers/record/8903956

Thesis

Quality assessment of protein structures using graph convolutional networks

Roy, Soumyadip, author; Ben-Hur, Asa, advisor; Blanchard, Nathaniel, committee member et al. · 2024

Full title: Quality assessment of protein structures using graph convolutional networks

Authors: Roy, Soumyadip, author; Ben-Hur, Asa, advisor; Blanchard, Nathaniel, committee member; Zhou, Wen, committee member

DOI: https://hdl.handle.net/10217/238364

Thesis

Adapting molecular docking to study sialylated glycans

Hu, Huimin · 2024

Full title: Adapting molecular docking to study sialylated glycans

Authors: Hu, Huimin

DOI: https://openscholar.uga.edu/record/8501/files/hu_huimin_201512_ms.pdf

Thesis

Accelerating Protein Design with Deep Learning

McPartlon, Matthew Timothy · 2023

Full title: Accelerating Protein Design with Deep Learning

Authors: McPartlon, Matthew Timothy

DOI: https://knowledge.uchicago.edu/record/7659/files/McPartlon_uchicago_0330D_16988.pdf

Thesis

Mechanistic Characterization and Development of Tailored Small Molecule Modulators of the κ-Opioid Receptor

Puls, Kristina · 2024

Full title: Mechanistic Characterization and Development of Tailored Small Molecule Modulators of the κ-Opioid Receptor

Authors: Puls, Kristina

DOI: https://refubium.fu-berlin.de/handle/fub188/43919

Thesis

Investigations on Key Principles of PTP1B Selectivity

Naß, Alexandra · 2018

Full title: Investigations on Key Principles of PTP1B Selectivity

Authors: Naß, Alexandra

DOI: https://refubium.fu-berlin.de/handle/fub188/22198

Thesis

Computational approaches exploring the structure and dynamics of ligand-gated ion channel receptors.

Chen, Zheng · 2023

Full title: Computational approaches exploring the structure and dynamics of ligand-gated ion channel receptors.

Authors: Chen, Zheng

DOI: https://hdl.handle.net/2123/31946

Thesis

The Pros and Cons of Backbone Flexibility in Molecular Dynamics Docking of Protein Complexes

Faruk, Nabil F. · 2022

Full title: The Pros and Cons of Backbone Flexibility in Molecular Dynamics Docking of Protein Complexes

Authors: Faruk, Nabil F.

DOI: https://knowledge.uchicago.edu/record/3630/files/Faruk_uchicago_0330D_16135.pdf

Thesis

Macromolecular Structure Prediction to Guide Studies of RNA Virus Proteins

Caballes, Raphael · 2025

Full title: Macromolecular Structure Prediction to Guide Studies of RNA Virus Proteins

Authors: Caballes, Raphael

DOI: http://hdl.handle.net/1959.4/105640

Thesis

Towards determination of binding poses of novel HIV-1 reverse transcriptase ligands using in silico methods

Dupree, Tom · 2018

Full title: Towards determination of binding poses of novel HIV-1 reverse transcriptase ligands using in silico methods

Authors: Dupree, Tom

DOI: http://hdl.handle.net/1959.4/60489

Thesis

Artificial Intelligence and High-Performance Computing for Accelerating Structure-Based Drug Discovery

Clyde, Austin Robert · 2022

Full title: Artificial Intelligence and High-Performance Computing for Accelerating Structure-Based Drug Discovery

Authors: Clyde, Austin Robert

DOI: https://knowledge.uchicago.edu/record/5266/files/Clyde_uchicago_0330D_16709.pdf

Thesis

Molecular models of NS3 protease variants of the Hepatitis C virus

da Silveira, NJF; Arcuri, H. A.; Bonalumi, C. E. et al. · 2014

Full title: Molecular models of NS3 protease variants of the Hepatitis C virus

Authors: da Silveira, NJF; Arcuri, H. A.; Bonalumi, C. E.; de Souza, F. P.; Mello, IMVGC; Rahal, Paula [UNESP]; Pinho, JRR; de Azevedo, W. F.

DOI: http://dx.doi.org/10.1186/1472-6807-5-1

Thesis

Natural Compounds as Non-Nucleoside Inhibitors of Zika Virus Polymerase through Integration of In Silico and In Vitro Approaches

Ramos, Paulo Ricardo Pimenta da Silva; Mottin, Melina; Lima, Caroline Sprengel [UNESP] et al. · 2023

Full title: Natural Compounds as Non-Nucleoside Inhibitors of Zika Virus Polymerase through Integration of In Silico and In Vitro Approaches

DOI: http://dx.doi.org/10.3390/ph15121493

Thesis

The impact of protein structure and sequence similarity on the accuracy of machine-learning scoring functions for binding affinity prediction

Li, Hongjian; Peng, Jiangjun; Leung, Yee et al. · 2024

Full title: The impact of protein structure and sequence similarity on the accuracy of machine-learning scoring functions for binding affinity prediction

Authors: Li, Hongjian; Peng, Jiangjun; Leung, Yee; Leung, Kwong-Sak; Wong, Man-Hon; Lu, Gang; Ballester, Pedro

DOI: https://www.mdpi.com/2218-273X/8/1/12

Thesis

Performance of machine-learning scoring functions in structure-based virtual screening

Wójcikowski, Maciej; Ballester, Pedro J; Siedlecki, Pawel · 2024

Full title: Performance of machine-learning scoring functions in structure-based virtual screening

Authors: Wójcikowski, Maciej; Ballester, Pedro J; Siedlecki, Pawel

DOI: https://doi.org/10.1038/srep46710

Thesis

Homology modeling informs ligand discovery for the glutamine transporter ASCT2

Garibsingh, RAA; Otte, NJ; Ndaru, E et al. · 2018

Full title: Homology modeling informs ligand discovery for the glutamine transporter ASCT2

Authors: Garibsingh, RAA; Otte, NJ; Ndaru, E; Colas, C; Grewer, C; Holst, J ; https://orcid.org/0000-0002-0377-9318; Schlessinger, A

DOI: http://hdl.handle.net/1959.4/unsworks_82529

Thesis

B-Cell Epitope Prediction for Improved Antibody Docking

Rontogiannis, Aristofanis · 2023

Full title: B-Cell Epitope Prediction for Improved Antibody Docking

Authors: Rontogiannis, Aristofanis

DOI: https://hdl.handle.net/1721.1/150148

Thesis

Biological vs. Crystallographic protein interfaces: An overview of computational approaches for their classification

Elez, Katarina; Bonvin, Alexandre M.J.J.; Vangone, Anna · 2020

Full title: Biological vs. Crystallographic protein interfaces: An overview of computational approaches for their classification

Authors: Elez, Katarina; Bonvin, Alexandre M.J.J.; Vangone, Anna

DOI: https://dspace.library.uu.nl/handle/1874/396135

Thesis

Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes.

Mikolajek, Halina; Weckener, Miriam; Brotzakis, Z Faidon et al. · 2022

Full title: Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes.

DOI: https://www.repository.cam.ac.uk/handle/1810/340308

Thesis

MolScore: a scoring, evaluation and benchmarking framework for generative models in de novo drug design

Thomas, Morgan; O'Boyle, Noel M; Bender, Andreas et al. · 2024

Full title: MolScore: a scoring, evaluation and benchmarking framework for generative models in de novo drug design

Authors: Thomas, Morgan; O'Boyle, Noel M; Bender, Andreas; De Graaf, Chris

DOI: https://www.repository.cam.ac.uk/handle/1810/369087

Thesis

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

Lensink, Marc F.; Velankar, Sameer; Kryshtafovych, Andriy et al. · 2016

Full title: Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

DOI: https://dspace.library.uu.nl/handle/1874/337451

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Reliability Of Alphafold Vs Experimental Structure

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