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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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NGLview-interactive molecular graphics for Jupyter notebooks

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

2018

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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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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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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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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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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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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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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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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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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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Development and testing of a general amber force field

Journal of computational chemistry, 2004-07, Vol.25 (9), p.1157-1174

2004

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A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site

PloS one, 2019-07, Vol.14 (7), p.e0219473-e0219473

2019

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The Amber biomolecular simulation programs

Journal of computational chemistry, 2005-12, Vol.26 (16), p.1668-1688

2005

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Constant pH molecular dynamics in generalized Born implicit solvent

Journal of computational chemistry, 2004-12, Vol.25 (16), p.2038-2048

2004

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The Dependence of Carbohydrate–Aromatic Interaction Strengths on the Structure of the Carbohydrate

Journal of the American Chemical Society, 2016-06, Vol.138 (24), p.7636-7648

2016

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Effective Born radii in the generalized Born approximation: The importance of being perfect

Journal of computational chemistry, 2002-11, Vol.23 (14), p.1297-1304

2002

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An accurate and simple quantum model for liquid water

The Journal of chemical physics, 2006-11, Vol.125 (18), p.184507-184507-11

2006

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Modification of the Generalized Born Model Suitable for Macromolecules

The journal of physical chemistry. B, 2000-04, Vol.104 (15), p.3712-3720

2000

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Generalized born models of macromolecular solvation effects

Annual review of physical chemistry, 2000-01, Vol.51 (1), p.129-152

2000

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HIV‑1 Capsid Function Is Regulated by Dynamics: Quantitative Atomic-Resolution Insights by Integrating Magic-Angle-Spinning NMR, QM/MM, and MD

Journal of the American Chemical Society, 2016-10, Vol.138 (42), p.14066-14075

2016

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An overview of the Amber biomolecular simulation package

NGLview-interactive molecular graphics for Jupyter notebooks

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

DOCK 6: Impact of new features and current docking performance

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

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

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

Molecular dynamics simulations of macromolecular crystals

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

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

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

Development and testing of a general amber force field

A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site

The Amber biomolecular simulation programs

Constant pH molecular dynamics in generalized Born implicit solvent

The Dependence of Carbohydrate–Aromatic Interaction Strengths on the Structure of the Carbohydrate

Effective Born radii in the generalized Born approximation: The importance of being perfect

An accurate and simple quantum model for liquid water

Modification of the Generalized Born Model Suitable for Macromolecules

Generalized born models of macromolecular solvation effects

HIV‑1 Capsid Function Is Regulated by Dynamics: Quantitative Atomic-Resolution Insights by Integrating Magic-Angle-Spinning NMR, QM/MM, and MD

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