PaperIdentification of novel triazolopyrimidines as potent α-glucosidase inhibitor through design, synthesis, biological evaluations, and computational analysis
Full title: Identification of novel triazolopyrimidines as potent α-glucosidase inhibitor through design, synthesis, biological evaluations, and computational analysis
PaperGeometry Optimization with Machine Trained Topological Atoms
Zielinski, François, Maxwell, Peter I., Fletcher, Timothy L., Davie, Stuart J., Pasquale, Nicodemo Di, Cardamone, Salvatore, Mills, Matthew J. L., Popelier, Paul L. A. · 2017 · Scientific Reports · DOI
Full title: Geometry Optimization with Machine Trained Topological Atoms
Authors: Zielinski, François, Maxwell, Peter I., Fletcher, Timothy L., Davie, Stuart J., Pasquale, Nicodemo Di, Cardamone, Salvatore, Mills, Matthew J. L., Popelier, Paul L. A.
PaperA comprehensive computational study to explore promising natural bioactive compounds targeting glycosyltransferase MurG in Escherichia coli for potential drug development
Shtaiwi, Amneh, Khan, Shafi Ullah, Khedraoui, Meriem, Alaraj, Mohd, Samadi, Abdelouahid, Chtita, Samir · 2024 · Scientific Reports · DOI
Full title: A comprehensive computational study to explore promising natural bioactive compounds targeting glycosyltransferase MurG in Escherichia coli for potential drug development
PaperComputational analysis of luteolin, apigenin and their derivatives from Allophylus africanus as potential inhibitors of plasmepsin II a malaria target
Abubakari, Ismail, Kwiyukwa, Lucas P., Paul, Lucas A. · 2025 · BMC Chemistry · DOI
Full title: Computational analysis of luteolin, apigenin and their derivatives from Allophylus africanus as potential inhibitors of plasmepsin II a malaria target
Authors: Abubakari, Ismail, Kwiyukwa, Lucas P., Paul, Lucas A.
PaperElucidation of α-glucosidase inhibitory activity and UHPLC-ESI-QTOF-MS based metabolic profiling of endophytic fungi Alternaria alternata BRN05 isolated from seeds of Swietenia macrophylla king
Kumar, Piyush, Kantari, Sai Anand Kannakazhi, Biswal, Ranendra Pratap, Ghanta, Prasanth, Dharanikota, Malleswara · 2025 · Frontiers in Fungal Biology · DOI
Full title: Elucidation of α-glucosidase inhibitory activity and UHPLC-ESI-QTOF-MS based metabolic profiling of endophytic fungi Alternaria alternata BRN05 isolated from seeds of Swietenia macrophylla king
PaperRevolutionizing diabetes treatment: computational insights into 4-hydroxy isoleucine derivatives and advanced molecular screening for antidiabetic compounds
Kelam, Lakshmi Mounika, Gill, Manjinder Singh, Sobhia, M. Elizabeth · 2025 · Exploration of Drug Science · DOI
Full title: Revolutionizing diabetes treatment: computational insights into 4-hydroxy isoleucine derivatives and advanced molecular screening for antidiabetic compounds
Authors: Kelam, Lakshmi Mounika, Gill, Manjinder Singh, Sobhia, M. Elizabeth
PaperIntegrative computational approaches for designing novel alpha-glucosidase inhibitors based on curculigoside A derivatives: Virtual screening, molecular docking, and molecular dynamics
Asnawi, Aiyi, Mieldianisa, Shifa, Aligita, Widhya, Yuliantini, Anne, Febrina, Ellin · 2024 · Journal of Herbmed Pharmacology · DOI
Full title: Integrative computational approaches for designing novel alpha-glucosidase inhibitors based on curculigoside A derivatives: Virtual screening, molecular docking, and molecular dynamics
PaperConformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory
Stylianakis, Ioannis, Zervos, Nikolaos, Lii, Jenn‐Huei, Pantazis, Dimitrios A., Kolocouris, Antonios · 2023 · Journal of Computer-Aided Molecular Design · DOI
Full title: Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory
ThesisMolecular simulations of carbohydrates with a fucose-binding Burkholderia ambifaria lectin suggest modulation by surface residues outside the fucose-binding pocket
Dingjan, T; Imberty, A; Pérez, S et al. · 2020 · University of Melbourne · DOI
Full title: Molecular simulations of carbohydrates with a fucose-binding Burkholderia ambifaria lectin suggest modulation by surface residues outside the fucose-binding pocket
ThesisMolecular dynamics simulation of inter-molecular interactions : a thesis submitted to Massey University in Albany, Auckland in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Computational Biochemistry
Shadfar, Shamim Zahra · 2020 · Massey University · DOI
Full title: Molecular dynamics simulation of inter-molecular interactions : a thesis submitted to Massey University in Albany, Auckland in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Computational Biochemistry
ThesisGalectin-1 binding to LacNAc and 3'-O-substituted LacNAc ligands:a study of non-covalent interactions in a lectin-carbohydrate complex
Ford, Michael Garrett · 2024 · University of Georgia - UGA Open Scholar · DOI
Full title: Galectin-1 binding to LacNAc and 3'-O-substituted LacNAc ligands:a study of non-covalent interactions in a lectin-carbohydrate complex
ThesisThe design and development of GPU accelerated algorithms for ab initio integrals and integral derivatives illustrated on ab initio quantum and hybrid QM/MM dynamics
Renison, Carina Alicia · 2017 · University of Cape Town · DOI
Full title: The design and development of GPU accelerated algorithms for ab initio integrals and integral derivatives illustrated on ab initio quantum and hybrid QM/MM dynamics
ThesisEnsemble methods in computational protein and ligand design : applications to the Fc[gamma] immunoglobulin, HIV-1 protease, and ketol-acid reductoisomerase systems
Silver, Nathaniel White · 2012 · Massachusetts Institute of Technology (MIT) · DOI
Full title: Ensemble methods in computational protein and ligand design : applications to the Fc[gamma] immunoglobulin, HIV-1 protease, and ketol-acid reductoisomerase systems
Authors: Silver, Nathaniel White
Year: 2012
Venue: Massachusetts Institute of Technology (MIT)
ThesisAn extended quantum mechanical molecular mechanics NWChem/AMBER interface for estimating free energies and determining reaction paths in catalytic enzymes: Application to cellulose degradation catalyzed by copper-dependent polysaccharide monooxygenases
Pirojsirikul, Teerapong · 2017 · University of California, San Diego (UCSD) · DOI
Full title: An extended quantum mechanical molecular mechanics NWChem/AMBER interface for estimating free energies and determining reaction paths in catalytic enzymes: Application to cellulose degradation catalyzed by copper-dependent polysaccharide monooxygenases
ThesisImprovements and Applications of Alchemical Free Energy, Constant pH and Accelerated Molecular Dynamics Calculations in the AMBER Molecular Dynamics Suite.
Mermelstein, Daniel Janson · 2018 · University of California, San Diego (UCSD) · DOI
Full title: Improvements and Applications of Alchemical Free Energy, Constant pH and Accelerated Molecular Dynamics Calculations in the AMBER Molecular Dynamics Suite.
ThesisApplications in QM and MM: the ab initio nanoreactor solves mechanisms in green and biological chemistry, and simulations probe the role of sialic acids in viral mechanisms
Oh, Lisa · 2022 · University of California, Davis · DOI
Full title: Applications in QM and MM: the ab initio nanoreactor solves mechanisms in green and biological chemistry, and simulations probe the role of sialic acids in viral mechanisms
ThesisComputational Simulations of Protein-Ligand Molecular Recognition via Enhanced Samplings, Free Energy Calculations and Applications to Structure-Based Drug Design
Park, In-Hee · 2010 · OhioLINK Electronic Theses and Dissertations · DOI
Full title: Computational Simulations of Protein-Ligand Molecular Recognition via Enhanced Samplings, Free Energy Calculations and Applications to Structure-Based Drug Design
Authors: Park, In-Hee
Year: 2010
Venue: OhioLINK Electronic Theses and Dissertations
ThesisExploring the interplay between experimental methods and the performance of predictors of binding affinity change upon mutations in protein complexes
Geng, Cunliang; Vangone, Anna; Bonvin, Alexandre M J J · 2016 · Utrecht University · DOI
Full title: Exploring the interplay between experimental methods and the performance of predictors of binding affinity change upon mutations in protein complexes
Authors: Geng, Cunliang; Vangone, Anna; Bonvin, Alexandre M J J
ThesisChemoenzymatic synthesis of complex N-glycans of the parasite S.mansoni to examine the importance of epitope presentation on DC-SIGN recognition
Srivastava, Apoorva D; Unione, Luca; Bunyatov, Mehman et al. · 2021 · Utrecht University · DOI
Full title: Chemoenzymatic synthesis of complex N-glycans of the parasite S.mansoni to examine the importance of epitope presentation on DC-SIGN recognition
ThesisNMR-based, molecular dynamics- and random walk molecular mechanics-supported study of conformational aspects of a carbohydrate ligand (Galβ1-2Galβ1-R) for an animal galectin in the free and in the bound state
Vliegenthart, J.F.G.; Siebert, H.-C; Gilleron, M. et al. · 1996 · Utrecht University · DOI
Full title: NMR-based, molecular dynamics- and random walk molecular mechanics-supported study of conformational aspects of a carbohydrate ligand (Galβ1-2Galβ1-R) for an animal galectin in the free and in the bound state
Authors: Vliegenthart, J.F.G.; Siebert, H.-C; Gilleron, M.; Kaltner, H.; Lieth, C.-W. von der; Kozár, T.; Bovin, N.; Korchagina, E.Y.
ThesisA new combined computational and NMR-spectroscopical strategy for the identification of additional conformational constraints of the bound ligand in an aprotic solvent
Vliegenthart, J.F.G.; Siebert, H.-C; André, S. et al. · 2000 · Utrecht University · DOI
Full title: A new combined computational and NMR-spectroscopical strategy for the identification of additional conformational constraints of the bound ligand in an aprotic solvent
Authors: Vliegenthart, J.F.G.; Siebert, H.-C; André, S.; Asensio, J.l.; Cañada, F.J.; Dong, X.; Espinosa, M.; Frank, M.
ThesisCH−π Interactions Are Required for Human Galectin-3 Function
Diehl, Roger C; Chorghade, Rajeev S; Keys, Allison M et al. · 2025 · Massachusetts Institute of Technology (MIT) · DOI
Full title: CH−π Interactions Are Required for Human Galectin-3 Function
Authors: Diehl, Roger C; Chorghade, Rajeev S; Keys, Allison M; Alam, Mohammad Murshid; Early, Stephen A; Dugan, Amanda E; Krupkin, Miri; Ribbeck, Katharina; Kulik, Heather J; Kiessling, Laura L
Year: 2025
Venue: Massachusetts Institute of Technology (MIT)
ThesisExamining the substrate specificity of the enzyme 3-O-sulfotransferase that regulates the biosynthesis of The anticoagulant heparan sulfate
Kim, Joo Kyung · 2024 · University of Georgia - UGA Open Scholar · DOI
Full title: Examining the substrate specificity of the enzyme 3-O-sulfotransferase that regulates the biosynthesis of The anticoagulant heparan sulfate
PaperAssessment of Binding Affinity via Alchemical Free-Energy Calculations
Kühn, Maximilian, Firth‐Clark, Stuart, Tosco, Paolo, Mey, Antonia S. J. S., Mackey, Mark, Michel, Julien · 2020 · Journal of Chemical Information and Modeling · DOI
Full title: Assessment of Binding Affinity via Alchemical Free-Energy Calculations
Authors: Kühn, Maximilian, Firth‐Clark, Stuart, Tosco, Paolo, Mey, Antonia S. J. S., Mackey, Mark, Michel, Julien
Year: 2020
Venue: Journal of Chemical Information and Modeling
PaperTheoretical Research of Interactions Between Glycosidases and Glycosaminoglycan Ligands with Molecular Docking and Molecular Dynamics Methods
Максименко, А. В. · 2020 · Cardiology and Cardiovascular Research · DOI
Full title: Theoretical Research of Interactions Between Glycosidases and Glycosaminoglycan Ligands with Molecular Docking and Molecular Dynamics Methods
PaperExploring the interactive mechanism of acarbose with the amylase SusG in the starch utilization system of the human gut symbiont <i>Bacteroides thetaiotaomicron</i> through molecular modeling
Kwain, Samuel, Dominy, Brian N., Whitehead, Kristi J., Miller, Brock A., Whitehead, Daniel C. · 2023 · Chemical Biology & Drug Design · DOI
Full title: Exploring the interactive mechanism of acarbose with the amylase SusG in the starch utilization system of the human gut symbiont <i>Bacteroides thetaiotaomicron</i> through molecular modeling
Authors: Kwain, Samuel, Dominy, Brian N., Whitehead, Kristi J., Miller, Brock A., Whitehead, Daniel C.
Full title: Integrative Approach for Designing Novel Triazole Derivatives as α-Glucosidase Inhibitors: QSAR, Molecular Docking, ADMET, and Molecular Dynamics Investigations
PaperSAMPL7 Host-Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations.
Amezcua, Martin; El Khoury, Léa; Mobley, David L · 2021 · Journal of computer-aided molecular design · DOI
Full title: SAMPL7 Host-Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations.
Authors: Amezcua, Martin; El Khoury, Léa; Mobley, David L
PaperImproving Speed and Affordability without Compromising Accuracy: Standard Binding Free-Energy Calculations Using an Enhanced Sampling Algorithm, Multiple-Time Stepping, and Hydrogen Mass Repartitioning.
Blazhynska, Marharyta; Goulard Coderc de Lacam, Emma; Chen, Haochuan et al. · 2023 · Journal of chemical theory and computation · DOI
Full title: Improving Speed and Affordability without Compromising Accuracy: Standard Binding Free-Energy Calculations Using an Enhanced Sampling Algorithm, Multiple-Time Stepping, and Hydrogen Mass Repartitioning.
ThesisThermodynamic and structural aspects of molecular recognition in mannose-binding protein complexes: a theoretical study over HRP-ArtinM association
Santo, Anderson Aparecido do Espirito [UNESP]; Feliciano, Gustavo Troiano [UNESP] · 2021 · Universidade Estadual Paulista (UNESP) · DOI
Full title: Thermodynamic and structural aspects of molecular recognition in mannose-binding protein complexes: a theoretical study over HRP-ArtinM association
Authors: Santo, Anderson Aparecido do Espirito [UNESP]; Feliciano, Gustavo Troiano [UNESP]
ThesisProtein evolution in the membrane of microscopic organisms: insights from gram-negative bacteria and SARS-CoV-2 through modeling and machine learning
Zhang, Zijian · 2025 · Georgia Institute of Technology · DOI
Full title: Protein evolution in the membrane of microscopic organisms: insights from gram-negative bacteria and SARS-CoV-2 through modeling and machine learning
ThesisChemoenzymatic synthesis of complex N-glycans of the parasite S.mansoni to examine the importance of epitope presentation on DC-SIGN recognition
Srivastava, Apoorva D; Unione, Luca; Bunyatov, Mehman et al. · 2021 · Utrecht University · DOI
Full title: Chemoenzymatic synthesis of complex N-glycans of the parasite S.mansoni to examine the importance of epitope presentation on DC-SIGN recognition
Identification of novel triazolopyrimidines as potent α-glucosidase inhibitor through design, synthesis, biological evaluations, and computational analysis
Full title: Identification of novel triazolopyrimidines as potent α-glucosidase inhibitor through design, synthesis, biological evaluations, and computational analysis
Geometry Optimization with Machine Trained Topological Atoms
Zielinski, François, Maxwell, Peter I., Fletcher, Timothy L., Davie, Stuart J., Pasquale, Nicodemo Di, Cardamone, Salvatore, Mills, Matthew J. L., Popelier, Paul L. A. · 2017
Full title: Geometry Optimization with Machine Trained Topological Atoms
Authors: Zielinski, François, Maxwell, Peter I., Fletcher, Timothy L., Davie, Stuart J., Pasquale, Nicodemo Di, Cardamone, Salvatore, Mills, Matthew J. L., Popelier, Paul L. A.
A comprehensive computational study to explore promising natural bioactive compounds targeting glycosyltransferase MurG in Escherichia coli for potential drug development
Full title: A comprehensive computational study to explore promising natural bioactive compounds targeting glycosyltransferase MurG in Escherichia coli for potential drug development
Computational analysis of luteolin, apigenin and their derivatives from Allophylus africanus as potential inhibitors of plasmepsin II a malaria target
Abubakari, Ismail, Kwiyukwa, Lucas P., Paul, Lucas A. · 2025
Full title: Computational analysis of luteolin, apigenin and their derivatives from Allophylus africanus as potential inhibitors of plasmepsin II a malaria target
Authors: Abubakari, Ismail, Kwiyukwa, Lucas P., Paul, Lucas A.
Elucidation of α-glucosidase inhibitory activity and UHPLC-ESI-QTOF-MS based metabolic profiling of endophytic fungi Alternaria alternata BRN05 isolated from seeds of Swietenia macrophylla king
Full title: Elucidation of α-glucosidase inhibitory activity and UHPLC-ESI-QTOF-MS based metabolic profiling of endophytic fungi Alternaria alternata BRN05 isolated from seeds of Swietenia macrophylla king
Revolutionizing diabetes treatment: computational insights into 4-hydroxy isoleucine derivatives and advanced molecular screening for antidiabetic compounds
Kelam, Lakshmi Mounika, Gill, Manjinder Singh, Sobhia, M. Elizabeth · 2025
Full title: Revolutionizing diabetes treatment: computational insights into 4-hydroxy isoleucine derivatives and advanced molecular screening for antidiabetic compounds
Authors: Kelam, Lakshmi Mounika, Gill, Manjinder Singh, Sobhia, M. Elizabeth
Integrative computational approaches for designing novel alpha-glucosidase inhibitors based on curculigoside A derivatives: Virtual screening, molecular docking, and molecular dynamics
Full title: Integrative computational approaches for designing novel alpha-glucosidase inhibitors based on curculigoside A derivatives: Virtual screening, molecular docking, and molecular dynamics
Full title: Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory
Molecular simulations of carbohydrates with a fucose-binding Burkholderia ambifaria lectin suggest modulation by surface residues outside the fucose-binding pocket
Dingjan, T; Imberty, A; Pérez, S et al. · 2020
Full title: Molecular simulations of carbohydrates with a fucose-binding Burkholderia ambifaria lectin suggest modulation by surface residues outside the fucose-binding pocket
Molecular dynamics simulation of inter-molecular interactions : a thesis submitted to Massey University in Albany, Auckland in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Computational Biochemistry
Shadfar, Shamim Zahra · 2020
Full title: Molecular dynamics simulation of inter-molecular interactions : a thesis submitted to Massey University in Albany, Auckland in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Computational Biochemistry
Galectin-1 binding to LacNAc and 3'-O-substituted LacNAc ligands:a study of non-covalent interactions in a lectin-carbohydrate complex
Ford, Michael Garrett · 2024
Full title: Galectin-1 binding to LacNAc and 3'-O-substituted LacNAc ligands:a study of non-covalent interactions in a lectin-carbohydrate complex
The design and development of GPU accelerated algorithms for ab initio integrals and integral derivatives illustrated on ab initio quantum and hybrid QM/MM dynamics
Renison, Carina Alicia · 2017
Full title: The design and development of GPU accelerated algorithms for ab initio integrals and integral derivatives illustrated on ab initio quantum and hybrid QM/MM dynamics
Ensemble methods in computational protein and ligand design : applications to the Fc[gamma] immunoglobulin, HIV-1 protease, and ketol-acid reductoisomerase systems
Silver, Nathaniel White · 2012
Full title: Ensemble methods in computational protein and ligand design : applications to the Fc[gamma] immunoglobulin, HIV-1 protease, and ketol-acid reductoisomerase systems
An extended quantum mechanical molecular mechanics NWChem/AMBER interface for estimating free energies and determining reaction paths in catalytic enzymes: Application to cellulose degradation catalyzed by copper-dependent polysaccharide monooxygenases
Pirojsirikul, Teerapong · 2017
Full title: An extended quantum mechanical molecular mechanics NWChem/AMBER interface for estimating free energies and determining reaction paths in catalytic enzymes: Application to cellulose degradation catalyzed by copper-dependent polysaccharide monooxygenases
Improvements and Applications of Alchemical Free Energy, Constant pH and Accelerated Molecular Dynamics Calculations in the AMBER Molecular Dynamics Suite.
Mermelstein, Daniel Janson · 2018
Full title: Improvements and Applications of Alchemical Free Energy, Constant pH and Accelerated Molecular Dynamics Calculations in the AMBER Molecular Dynamics Suite.
Applications in QM and MM: the ab initio nanoreactor solves mechanisms in green and biological chemistry, and simulations probe the role of sialic acids in viral mechanisms
Oh, Lisa · 2022
Full title: Applications in QM and MM: the ab initio nanoreactor solves mechanisms in green and biological chemistry, and simulations probe the role of sialic acids in viral mechanisms
Computational Simulations of Protein-Ligand Molecular Recognition via Enhanced Samplings, Free Energy Calculations and Applications to Structure-Based Drug Design
Park, In-Hee · 2010
Full title: Computational Simulations of Protein-Ligand Molecular Recognition via Enhanced Samplings, Free Energy Calculations and Applications to Structure-Based Drug Design
Full title: Exploring the interplay between experimental methods and the performance of predictors of binding affinity change upon mutations in protein complexes
Authors: Geng, Cunliang; Vangone, Anna; Bonvin, Alexandre M J J
Full title: Chemoenzymatic synthesis of complex N-glycans of the parasite S.mansoni to examine the importance of epitope presentation on DC-SIGN recognition
NMR-based, molecular dynamics- and random walk molecular mechanics-supported study of conformational aspects of a carbohydrate ligand (Galβ1-2Galβ1-R) for an animal galectin in the free and in the bound state
Vliegenthart, J.F.G.; Siebert, H.-C; Gilleron, M. et al. · 1996
Full title: NMR-based, molecular dynamics- and random walk molecular mechanics-supported study of conformational aspects of a carbohydrate ligand (Galβ1-2Galβ1-R) for an animal galectin in the free and in the bound state
Authors: Vliegenthart, J.F.G.; Siebert, H.-C; Gilleron, M.; Kaltner, H.; Lieth, C.-W. von der; Kozár, T.; Bovin, N.; Korchagina, E.Y.
A new combined computational and NMR-spectroscopical strategy for the identification of additional conformational constraints of the bound ligand in an aprotic solvent
Vliegenthart, J.F.G.; Siebert, H.-C; André, S. et al. · 2000
Full title: A new combined computational and NMR-spectroscopical strategy for the identification of additional conformational constraints of the bound ligand in an aprotic solvent
Authors: Vliegenthart, J.F.G.; Siebert, H.-C; André, S.; Asensio, J.l.; Cañada, F.J.; Dong, X.; Espinosa, M.; Frank, M.
CH−π Interactions Are Required for Human Galectin-3 Function
Diehl, Roger C; Chorghade, Rajeev S; Keys, Allison M et al. · 2025
Full title: CH−π Interactions Are Required for Human Galectin-3 Function
Authors: Diehl, Roger C; Chorghade, Rajeev S; Keys, Allison M; Alam, Mohammad Murshid; Early, Stephen A; Dugan, Amanda E; Krupkin, Miri; Ribbeck, Katharina; Kulik, Heather J; Kiessling, Laura L
Examining the substrate specificity of the enzyme 3-O-sulfotransferase that regulates the biosynthesis of The anticoagulant heparan sulfate
Kim, Joo Kyung · 2024
Full title: Examining the substrate specificity of the enzyme 3-O-sulfotransferase that regulates the biosynthesis of The anticoagulant heparan sulfate