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Generalized Born Implicit Solvent Models for Biomolecules

Annual review of biophysics, 2019-05, Vol.48 (1), p.275-296

2019

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An overview of the Amber biomolecular simulation package

Wiley interdisciplinary reviews. Computational molecular science, 2013-03, Vol.3 (2), p.198-210

2013

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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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NGLview-interactive molecular graphics for Jupyter notebooks

Bioinformatics, 2018-04, Vol.34 (7), p.1241-1242

2018

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DOCK 6: Impact of new features and current docking performance

Journal of computational chemistry, 2015-06, Vol.36 (15), p.1132-1156

2015

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Parmbsc1: a refined force field for DNA simulations

Nature methods, 2016-01, Vol.13 (1), p.55-58

2016

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Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

Journal of computer-aided molecular design, 2017-01, Vol.31 (1), p.147-161

2017

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Soft-core potentials in thermodynamic integration: Comparing one- and two-step transformations

Journal of computational chemistry, 2011-11, Vol.32 (15), p.3253-3263

2011

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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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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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Diffuse X-ray scattering from correlated motions in a protein crystal

Nature communications, 2020-03, Vol.11 (1), p.1271-1271, Article 1271

2020

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Robust total X-ray scattering workflow to study correlated motion of proteins in crystals

Nature communications, 2023-03, Vol.14 (1), p.1228-1228, Article 1228

2023

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Automatic atom type and bond type perception in molecular mechanical calculations

Journal of molecular graphics & modelling, 2006-10, Vol.25 (2), p.247-260

2006

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Predicting Site-Binding Modes of Ions and Water to Nucleic Acids Using Molecular Solvation Theory

Journal of the American Chemical Society, 2019-02, Vol.141 (6), p.2435-2445

2019

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Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations

The Journal of chemical physics, 2007-12, Vol.127 (21), p.214108-214108

2007

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Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction

Nature communications, 2020-11, Vol.11 (1), p.5531-14, Article 5531

2020

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Twenty-five years of nucleic acid simulations

Biopolymers, 2013-12, Vol.99 (12), p.969-977

2013

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Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf

Journal of computational chemistry, 2004-01, Vol.25 (2), p.238-250

2004

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Structure of the HIV-1 RNA packaging signal

Science (American Association for the Advancement of Science), 2015-05, Vol.348 (6237), p.917-921

2015

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An RNA excited conformational state at atomic resolution

Nature communications, 2023-12, Vol.14 (1), p.8432-8432, Article 8432

2023

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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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Structural basis for transcriptional start site control of HIV-1 RNA fate

Science (American Association for the Advancement of Science), 2020-04, Vol.368 (6489), p.413-417

2020

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Resolving Ambiguous Protonation and Oxidation States in the Oxygen Evolving Complex of Photosystem II

The journal of physical chemistry. B, 2018-09, Vol.122 (37), p.8654-8664

2018

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implementation of a fast and accurate QM/MM potential method in Amber

Journal of computational chemistry, 2008-05, Vol.29 (7), p.1019-1031

2008

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Simple electrolyte solutions: comparison of DRISM and molecular dynamics results for alkali halide solutions

The Journal of chemical physics, 2013-01, Vol.138 (4), p.044103-044103

2013

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Generalized Born Implicit Solvent Models for Biomolecules

An overview of the Amber biomolecular simulation package

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

NGLview-interactive molecular graphics for Jupyter notebooks

DOCK 6: Impact of new features and current docking performance

Parmbsc1: a refined force field for DNA simulations

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

Soft-core potentials in thermodynamic integration: Comparing one- and two-step transformations

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

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

Diffuse X-ray scattering from correlated motions in a protein crystal

Robust total X-ray scattering workflow to study correlated motion of proteins in crystals

Automatic atom type and bond type perception in molecular mechanical calculations

Predicting Site-Binding Modes of Ions and Water to Nucleic Acids Using Molecular Solvation Theory

Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations

Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction

Twenty-five years of nucleic acid simulations

Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf

Structure of the HIV-1 RNA packaging signal

An RNA excited conformational state at atomic resolution

Molecular dynamics simulations of macromolecular crystals

Structural basis for transcriptional start site control of HIV-1 RNA fate

Resolving Ambiguous Protonation and Oxidation States in the Oxygen Evolving Complex of Photosystem II

implementation of a fast and accurate QM/MM potential method in Amber

Simple electrolyte solutions: comparison of DRISM and molecular dynamics results for alkali halide solutions

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