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CHARMM‐GUI ligand reader and modeler for CHARMM force field generation of small molecules

Journal of computational chemistry, 2017-08, Vol.38 (21), p.1879-1886

2017

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FASTDock: A Pipeline for Allosteric Drug Discovery

Journal of chemical information and modeling, 2023-11, Vol.63 (22), p.7219-7227

2023

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CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

Journal of chemical theory and computation, 2016-01, Vol.12 (1), p.405-413

2016

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Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM

Journal of computational chemistry, 2016-03, Vol.37 (8), p.753-762

2016

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WExplore: Hierarchical Exploration of High-Dimensional Spaces Using the Weighted Ensemble Algorithm

The journal of physical chemistry. B, 2014-04, Vol.118 (13), p.3532-3542

2014

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M2 amphipathic helices facilitate pH-dependent conformational transition in influenza A virus

Proceedings of the National Academy of Sciences - PNAS, 2020-02, Vol.117 (7), p.3583-3591

2020

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Automated, Accurate, and Scalable Relative Protein–Ligand Binding Free-Energy Calculations Using Lambda Dynamics

Journal of chemical theory and computation, 2020-12, Vol.16 (12), p.7895-7914

2020

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Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand–protein interactions

Bioorganic & medicinal chemistry, 2016-10, Vol.24 (20), p.4812-4825

2016

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A strategy for proline and glycine mutations to proteins with alchemical free energy calculations

Journal of computational chemistry, 2021-06, Vol.42 (15), p.1088-1094

2021

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Selection pressures on evolution of ribonuclease H explored with rigorous free-energy-based design

Proceedings of the National Academy of Sciences - PNAS, 2024-01, Vol.121 (3), p.e2312029121

2024

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Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism

Proceedings of the National Academy of Sciences - PNAS, 2007-11, Vol.104 (47), p.18496-18501

2007

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Classical molecular dynamics

The Journal of chemical physics, 2021-03, Vol.154 (10), p.100401-100401

2021

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Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism

Proteins, structure, function, and bioinformatics, 2014-07, Vol.82 (7), p.1319-1331

2014

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Membrane environment modulates the pKa values of transmembrane helices

The journal of physical chemistry. B, 2015-04, Vol.119 (13), p.4601-4607

2015

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Accelerated CDOCKER with GPUs, Parallel Simulated Annealing, and Fast Fourier Transforms

Journal of chemical theory and computation, 2020-06, Vol.16 (6), p.3910-3919

2020

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Free Gangliosides Can Alter Amyloid‑β Aggregation

The journal of physical chemistry letters, 2022-10, Vol.13 (40), p.9303-9308

2022

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Fast Solver for Large Scale Multistate Bennett Acceptance Ratio Equations

Journal of chemical theory and computation, 2019-02, Vol.15 (2), p.799-802

2019

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Adaptive Landscape Flattening Accelerates Sampling of Alchemical Space in Multisite λ Dynamics

The journal of physical chemistry. B, 2017-04, Vol.121 (15), p.3626-3635

2017

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Crowding Induced Collective Hydration of Biological Macromolecules over Extended Distances

Journal of the American Chemical Society, 2014-01, Vol.136 (1), p.188-194

2014

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λ-Dynamics free energy simulation methods

Journal of computational chemistry, 2009-08, Vol.30 (11), p.1692-1700

2009

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Recent advances in implicit solvent-based methods for biomolecular simulations

Current opinion in structural biology, 2008-04, Vol.18 (2), p.140-148

2008

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Extending the treatment of backbone energetics in protein force fields: Limitations of gas‐phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

Journal of computational chemistry, 2004-08, Vol.25 (11), p.1400-1415

2004

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Investigating the Effect of Two-Point Surface Attachment on Enzyme Stability and Activity

Journal of the American Chemical Society, 2018-12, Vol.140 (48), p.16560-16569

2018

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A modified TIP3P water potential for simulation with Ewald summation

The Journal of chemical physics, 2004-11, Vol.121 (20), p.10096-10103

2004

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Exploring the Limits of the Generalized CHARMM and AMBER Force Fields through Predictions of Hydration Free Energy of Small Molecules

Journal of chemical information and modeling, 2024-05, Vol.64 (10), p.4089-4101

2024

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CHARMM‐GUI ligand reader and modeler for CHARMM force field generation of small molecules

FASTDock: A Pipeline for Allosteric Drug Discovery

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM

WExplore: Hierarchical Exploration of High-Dimensional Spaces Using the Weighted Ensemble Algorithm

M2 amphipathic helices facilitate pH-dependent conformational transition in influenza A virus

Automated, Accurate, and Scalable Relative Protein–Ligand Binding Free-Energy Calculations Using Lambda Dynamics

Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand–protein interactions

A strategy for proline and glycine mutations to proteins with alchemical free energy calculations

Selection pressures on evolution of ribonuclease H explored with rigorous free-energy-based design

Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism

Classical molecular dynamics

Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism

Membrane environment modulates the pKa values of transmembrane helices

Accelerated CDOCKER with GPUs, Parallel Simulated Annealing, and Fast Fourier Transforms

Free Gangliosides Can Alter Amyloid‑β Aggregation

Fast Solver for Large Scale Multistate Bennett Acceptance Ratio Equations

Adaptive Landscape Flattening Accelerates Sampling of Alchemical Space in Multisite λ Dynamics

Crowding Induced Collective Hydration of Biological Macromolecules over Extended Distances

λ-Dynamics free energy simulation methods

Recent advances in implicit solvent-based methods for biomolecular simulations

Extending the treatment of backbone energetics in protein force fields: Limitations of gas‐phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

Investigating the Effect of Two-Point Surface Attachment on Enzyme Stability and Activity

A modified TIP3P water potential for simulation with Ewald summation

Exploring the Limits of the Generalized CHARMM and AMBER Force Fields through Predictions of Hydration Free Energy of Small Molecules

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