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GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features

Journal of chemical information and modeling, 2018-10, Vol.58 (10), p.2043-2050

2018

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OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins

Journal of chemical theory and computation, 2016-01, Vol.12 (1), p.281-296

2016

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Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model

Journal of chemical theory and computation, 2016-08, Vol.12 (8), p.3926-3947

2016

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Molecular dynamics simulations of macromolecular crystals

Wiley interdisciplinary reviews. Computational molecular science, 2019-07, Vol.9 (4), p.e1402-n/a

2019

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Histidine protonation controls structural heterogeneity in the cyanobacteriochrome AnPixJg2

Physical chemistry chemical physics : PCCP, 2021-03, Vol.23 (12), p.7359-7367

2021

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STORMM: Structure and topology replica molecular mechanics for chemical simulations

The Journal of chemical physics, 2024-07, Vol.161 (3)

2024

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AmberTools

Journal of chemical information and modeling, 2023-10, Vol.63 (20), p.6183-6191

2023

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Simulations of a Protein Crystal: Explicit Treatment of Crystallization Conditions Links Theory and Experiment in the Streptavidin−Biotin Complex

Biochemistry (Easton), 2008-11, Vol.47 (46), p.12065-12077

2008

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Dynamics of the Streptavidin−Biotin Complex in Solution and in Its Crystal Lattice: Distinct Behavior Revealed by Molecular Simulations

The journal of physical chemistry. B, 2009-05, Vol.113 (19), p.6971-6985

2009

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ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins

Journal of chemical theory and computation, 2014-10, Vol.10 (10), p.4515-4534

2014

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Derivation of Fixed Partial Charges for Amino Acids Accommodating a Specific Water Model and Implicit Polarization

The journal of physical chemistry. B, 2013-02, Vol.117 (8), p.2328-2338

2013

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Correction: Histidine protonation controls structural heterogeneity in the cyanobacteriochrome AnPixJg2

Physical chemistry chemical physics : PCCP, 2021-06, Vol.23 (21), p.12494-12494

2021

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Fast Implementation of the Nudged Elastic Band Method in AMBER

Journal of chemical theory and computation, 2019-08, Vol.15 (8), p.4699-4707

2019

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Second-Contact Shell Mutation Diminishes Streptavidin–Biotin Binding Affinity through Transmitted Effects on Equilibrium Dynamics

Biochemistry (Easton), 2012-01, Vol.51 (2), p.597-607

2012

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Configurational‐bias sampling technique for predicting side‐chain conformations in proteins

Protein science, 2006-09, Vol.15 (9), p.2029-2039

2006

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Peptide Crystal Simulations Reveal Hidden Dynamics

Journal of the American Chemical Society, 2013-05, Vol.135 (21), p.7938-7948

2013

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Staggered Mesh Ewald: An Extension of the Smooth Particle-Mesh Ewald Method Adding Great Versatility

Journal of chemical theory and computation, 2009-09, Vol.5 (9), p.2322-2338

2009

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A twist in the road less traveled: The AMBER ff15ipq-m force field for protein mimetics

The Journal of chemical physics, 2020-08, Vol.153 (6), p.064101-064101

2020

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On the fly estimation of host–guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge

Journal of computer-aided molecular design, 2017, Vol.31 (1), p.47-60

2017

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Alchemical prediction of hydration free energies for SAMPL

Journal of computer-aided molecular design, 2012-05, Vol.26 (5), p.551-562

2012

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Simulations of a Protein Crystal with a High Resolution X-ray Structure: Evaluation of Force Fields and Water Models

The journal of physical chemistry. B, 2010-10, Vol.114 (40), p.12811-12824

2010

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Links between the charge model and bonded parameter force constants in biomolecular force fields

The Journal of chemical physics, 2017-10, Vol.147 (16), p.161730-161730

2017

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A Vulnerability in Popular Molecular Dynamics Packages Concerning Langevin and Andersen Dynamics

Journal of chemical theory and computation, 2008-10, Vol.4 (10), p.1669-1680

2008

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Multi-Level Ewald: A Hybrid Multigrid/Fast Fourier Transform Approach to the Electrostatic Particle-Mesh Problem

Journal of chemical theory and computation, 2010-02, Vol.6 (2), p.443-458

2010

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Rapid Estimation of Solvation Energy for Simulations of Protein−Protein Association

Journal of chemical theory and computation, 2005-01, Vol.1 (1), p.143-152

2005

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GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features

OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins

Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model

Molecular dynamics simulations of macromolecular crystals

Histidine protonation controls structural heterogeneity in the cyanobacteriochrome AnPixJg2

STORMM: Structure and topology replica molecular mechanics for chemical simulations

AmberTools

Simulations of a Protein Crystal: Explicit Treatment of Crystallization Conditions Links Theory and Experiment in the Streptavidin−Biotin Complex

Dynamics of the Streptavidin−Biotin Complex in Solution and in Its Crystal Lattice: Distinct Behavior Revealed by Molecular Simulations

ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins

Derivation of Fixed Partial Charges for Amino Acids Accommodating a Specific Water Model and Implicit Polarization

Correction: Histidine protonation controls structural heterogeneity in the cyanobacteriochrome AnPixJg2

Fast Implementation of the Nudged Elastic Band Method in AMBER

Second-Contact Shell Mutation Diminishes Streptavidin–Biotin Binding Affinity through Transmitted Effects on Equilibrium Dynamics

Configurational‐bias sampling technique for predicting side‐chain conformations in proteins

Peptide Crystal Simulations Reveal Hidden Dynamics

Staggered Mesh Ewald: An Extension of the Smooth Particle-Mesh Ewald Method Adding Great Versatility

A twist in the road less traveled: The AMBER ff15ipq-m force field for protein mimetics

On the fly estimation of host–guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge

Alchemical prediction of hydration free energies for SAMPL

Simulations of a Protein Crystal with a High Resolution X-ray Structure: Evaluation of Force Fields and Water Models

Links between the charge model and bonded parameter force constants in biomolecular force fields

A Vulnerability in Popular Molecular Dynamics Packages Concerning Langevin and Andersen Dynamics

Multi-Level Ewald: A Hybrid Multigrid/Fast Fourier Transform Approach to the Electrostatic Particle-Mesh Problem

Rapid Estimation of Solvation Energy for Simulations of Protein−Protein Association

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