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Molecular dynamics simulations of protein dynamics and their relevance to drug discovery

Current opinion in pharmacology, 2010-12, Vol.10 (6), p.738-744

Salsbury, Freddie R

2010

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Experimentally Dissecting the Origins of Peroxiredoxin Catalysis

Antioxidants & redox signaling, 2018-03, Vol.28 (7), p.521-536

2018

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New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations

Journal of computational chemistry, 2003-08, Vol.24 (11), p.1348-1356

2003

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Constant-pH molecular dynamics using continuous titration coordinates

Proteins, structure, function, and bioinformatics, 2004-09, Vol.56 (4), p.738-752

2004

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Applying physics-based scoring to calculate free energies of binding for single amino acid mutations in protein-protein complexes

PloS one, 2013-12, Vol.8 (12), p.e82849-e82849

2013

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The Stability of a Model Substrate for Topoisomerase 1-Mediated DNA Religation Depends on the Presence of Mismatched Base Pairs

Journal of Nucleic Acids, 2011-01, Vol.2011 (2011), p.211-218

2011

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An efficient hybrid explicit/implicit solvent method for biomolecular simulations

Journal of computational chemistry, 2004-12, Vol.25 (16), p.1967-1978

2004

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In silico and in vivo anti-malarial studies of 18β glycyrrhetinic acid from Glycyrrhiza glabra

PloS one, 2013-09, Vol.8 (9), p.e74761

2013

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Alternative computational protocols for supercharging protein surfaces for reversible unfolding and retention of stability

PloS one, 2013-05, Vol.8 (5), p.e64363-e64363

2013

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Chiral ruthenium(II) polypyridyl complexes: stabilization of g-quadruplex DNA, inhibition of telomerase activity and cellular uptake

PloS one, 2012-12, Vol.7 (12), p.e50902-e50902

2012

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A wrench in the works of human acetylcholinesterase: soman induced conformational changes revealed by molecular dynamics simulations

PloS one, 2015-04, Vol.10 (4), p.e0121092-e0121092

2015

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Electrostatics of cysteine residues in proteins: Parameterization and validation of a simple model

Proteins, structure, function, and bioinformatics, 2012-11, Vol.80 (11), p.2583-2591

2012

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High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics

PloS one, 2015-04, Vol.10 (4), p.e0123146-e0123146

2015

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An Algorithm for Protein Helix Assignment Using Helix Geometry

PloS one, 2015-07, Vol.10 (7), p.e0129674-e0129674

2015

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Unraveling the Role of Hydrogen Bonds in Thrombin via Two Machine Learning Methods

Journal of chemical information and modeling, 2023-06, Vol.63 (12), p.3705-3718

2023

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Light Chain Mutation Effects on the Dynamics of Thrombin

Journal of chemical information and modeling, 2021-02, Vol.61 (2), p.950-965

2021

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Computational study on the different ligands induced conformation change of β2 adrenergic receptor-Gs protein complex

PloS one, 2013-07, Vol.8 (7), p.e68138-e68138

2013

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Structural Insight into Melatonin's Influence on the Conformation of Aβ42 Dimer Studied by Molecular Dynamics Simulation

The journal of physical chemistry. B, 2024-10, Vol.128 (41), p.9947

2024

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Structural Insight into Melatonin’s Influence on the Conformation of Aβ 42 Dimer Studied by Molecular Dynamics Simulation

The journal of physical chemistry. B, 2024-10, Vol.128 (41), p.9947-9958

2024

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Structural Variabilities in β-Lactamase (blaA) of Different Biovars of Yersinia enterocolitica: Implications for β-Lactam Antibiotic and β-Lactamase Inhibitor Susceptibilities

PloS one, 2015-04, Vol.10 (4), p.e0123564-e0123564

2015

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Autoinhibitory mechanisms of ERG studied by molecular dynamics simulations

AIP advances, 2015-01, Vol.5 (1), p.017130-017130

2015

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Differences in the binding affinities of ErbB family: heterogeneity in the prediction of resistance mutants

PloS one, 2013-10, Vol.8 (10), p.e77054-e77054

2013

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Thrombin - A Molecular Dynamics Perspective

Mini reviews in medicinal chemistry, 2024-01, Vol.24 (11), p.1112-1124

2024

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Ligand-induced conformational selection predicts the selectivity of cysteine protease inhibitors

PloS one, 2019-12, Vol.14 (12), p.e0222055-e0222055

2019

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Biapenem inactivation by B2 metallo β-lactamases: energy landscape of the hydrolysis reaction

PloS one, 2013, Vol.8 (1), p.e55136-e55136

2013

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Molecular dynamics simulations of protein dynamics and their relevance to drug discovery

Experimentally Dissecting the Origins of Peroxiredoxin Catalysis

New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations

Constant-pH molecular dynamics using continuous titration coordinates

Applying physics-based scoring to calculate free energies of binding for single amino acid mutations in protein-protein complexes

The Stability of a Model Substrate for Topoisomerase 1-Mediated DNA Religation Depends on the Presence of Mismatched Base Pairs

An efficient hybrid explicit/implicit solvent method for biomolecular simulations

In silico and in vivo anti-malarial studies of 18β glycyrrhetinic acid from Glycyrrhiza glabra

Alternative computational protocols for supercharging protein surfaces for reversible unfolding and retention of stability

Chiral ruthenium(II) polypyridyl complexes: stabilization of g-quadruplex DNA, inhibition of telomerase activity and cellular uptake

A wrench in the works of human acetylcholinesterase: soman induced conformational changes revealed by molecular dynamics simulations

Electrostatics of cysteine residues in proteins: Parameterization and validation of a simple model

High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics

An Algorithm for Protein Helix Assignment Using Helix Geometry

Unraveling the Role of Hydrogen Bonds in Thrombin via Two Machine Learning Methods

Light Chain Mutation Effects on the Dynamics of Thrombin

Computational study on the different ligands induced conformation change of β2 adrenergic receptor-Gs protein complex

Structural Insight into Melatonin's Influence on the Conformation of Aβ42 Dimer Studied by Molecular Dynamics Simulation

Structural Insight into Melatonin’s Influence on the Conformation of Aβ 42 Dimer Studied by Molecular Dynamics Simulation

Structural Variabilities in β-Lactamase (blaA) of Different Biovars of Yersinia enterocolitica: Implications for β-Lactam Antibiotic and β-Lactamase Inhibitor Susceptibilities

Autoinhibitory mechanisms of ERG studied by molecular dynamics simulations

Differences in the binding affinities of ErbB family: heterogeneity in the prediction of resistance mutants

Thrombin - A Molecular Dynamics Perspective

Ligand-induced conformational selection predicts the selectivity of cysteine protease inhibitors

Biapenem inactivation by B2 metallo β-lactamases: energy landscape of the hydrolysis reaction

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