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PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

Journal of chemical theory and computation, 2013-07, Vol.9 (7), p.3084-3095

2013

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Assessing the Current State of Amber Force Field Modifications for DNA

Journal of chemical theory and computation, 2016-08, Vol.12 (8), p.4114-4127

2016

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Quantum mechanically derived AMBER-compatible heme parameters for various states of the cytochrome P450 catalytic cycle

Journal of computational chemistry, 2012-01, Vol.33 (2), p.119-133

2012

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Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B‑DNA

Journal of chemical theory and computation, 2015-12, Vol.11 (12), p.5723-5736

2015

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Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)

Biochimica et biophysica acta, 2015-05, Vol.1850 (5), p.1041-1058

2015

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Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters

The journal of physical chemistry. B, 2009-10, Vol.113 (40), p.13279-13290

2009

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Benchmarking the Drude Polarizable Force Field Using the r(GACC) Tetranucleotide

Journal of chemical information and modeling, 2023-04, Vol.63 (8), p.2505-2511

2023

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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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Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

The journal of physical chemistry. B, 2008-07, Vol.112 (30), p.9020-9041

2008

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Parallelization of CPPTRAJ enables large scale analysis of molecular dynamics trajectory data

Journal of computational chemistry, 2018-09, Vol.39 (25), p.2110-2117

2018

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Assessment of A- to B- DNA Transitions Utilizing the Drude Polarizable Force Field

Journal of chemical theory and computation, 2023-12, Vol.19 (23), p.8955-8966

2023

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Structures and Dynamics of DNA Mini-Dumbbells Are Force Field Dependent

Journal of chemical theory and computation, 2023-04, Vol.19 (8), p.2198-2212

2023

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van der Waals Parameter Scanning with Amber Nucleic Acid Force Fields: Revisiting Means to Better Capture the RNA/DNA Structure through MD

Journal of chemical theory and computation, 2024-01, Vol.20 (2), p.625-643

2024

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Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

Journal of chemical theory and computation, 2011-09, Vol.7 (9), p.2886-2902

2011

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Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields

RNA (Cambridge), 2015-09, Vol.21 (9), p.1578-1590

2015

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Improved Force Field Parameters Lead to a Better Description of RNA Structure

Journal of chemical theory and computation, 2015-09, Vol.11 (9), p.3969-3972

2015

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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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Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters

Journal of chemical theory and computation, 2013-05, Vol.9 (5), p.2339-2354

2013

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Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations

Biochimie, 2014-10, Vol.105, p.22-35

2014

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Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide

Journal of chemical theory and computation, 2014-01, Vol.10 (1), p.492-499

2014

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Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms

Journal of chemical theory and computation, 2007-11, Vol.3 (6), p.2312-2334

2007

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Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins

Journal of chemical theory and computation, 2010-12, Vol.6 (12), p.3836-3849

2010

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Molecular basis for the broad substrate selectivity of a peptide prenyltransferase

Proceedings of the National Academy of Sciences - PNAS, 2016-12, Vol.113 (49), p.14037-14042

2016

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Assessing the Current State of Amber Force Field Modifications for DNA2023 Edition

Journal of chemical theory and computation, 2023-07, Vol.19 (13), p.4299-4307

2023

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Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/ γ Conformers

Biophysical journal, 2007-06, Vol.92 (11), p.3817-3829

2007

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PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

Assessing the Current State of Amber Force Field Modifications for DNA

Quantum mechanically derived AMBER-compatible heme parameters for various states of the cytochrome P450 catalytic cycle

Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B‑DNA

Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)

Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters

Benchmarking the Drude Polarizable Force Field Using the r(GACC) Tetranucleotide

Twenty-five years of nucleic acid simulations

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

Parallelization of CPPTRAJ enables large scale analysis of molecular dynamics trajectory data

Assessment of A- to B- DNA Transitions Utilizing the Drude Polarizable Force Field

Structures and Dynamics of DNA Mini-Dumbbells Are Force Field Dependent

van der Waals Parameter Scanning with Amber Nucleic Acid Force Fields: Revisiting Means to Better Capture the RNA/DNA Structure through MD

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields

Improved Force Field Parameters Lead to a Better Description of RNA Structure

The Amber biomolecular simulation programs

Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters

Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations

Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide

Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms

Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins

Molecular basis for the broad substrate selectivity of a peptide prenyltransferase

Assessing the Current State of Amber Force Field Modifications for DNA2023 Edition

Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/ γ Conformers

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