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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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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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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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Twenty-five years of nucleic acid simulations

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

2013

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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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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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Molecular dynamics simulation of triclinic lysozyme in a crystal lattice

Protein science, 2016-01, Vol.25 (1), p.87-102

2016

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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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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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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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Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures

Journal of computational chemistry, 2004-01, Vol.25 (2), p.265-284

2004

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Molecular dynamics analysis of a flexible loop at the binding interface of the SARS‐CoV‐2 spike protein receptor‐binding domain

Proteins, structure, function, and bioinformatics, 2022-05, Vol.90 (5), p.1044-1053

2022

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Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods

Biopolymers, 2003-01, Vol.68 (1), p.16-34

2003

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Change in protein flexibility upon complex formation: Analysis of Ras-Raf using molecular dynamics and a molecular framework approach

Proteins, structure, function, and bioinformatics, 2004-08, Vol.56 (2), p.322-337

2004

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Exploring protein native states and large-scale conformational changes with a modified generalized born model

Proteins, structure, function, and bioinformatics, 2004-05, Vol.55 (2), p.383-394

2004

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Correlated motions in enzymes

The FASEB journal, 2022-05, Vol.36 (S1), p.n/a

2022

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Enhanced TROSY Effect in [2‐19F, 2‐13C] Adenosine and ATP Analogs Facilitates NMR Spectroscopy of Very Large Biological RNAs in Solution

Angewandte Chemie International Edition, 2024-02, Vol.63 (9), p.e202316273-n/a

International ed. in English, 2024

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New experimental evidence for pervasive dynamics in proteins

Protein science, 2023-05, Vol.32 (5), p.e4630-n/a

2023

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Second derivatives in generalized Born theory

Journal of computational chemistry, 2006-11, Vol.27 (14), p.1662-1675

2006

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Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix

Acta crystallographica. Section D, Biological crystallography., 2020-01, Vol.76 (1), p.51-62

2020

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Homology Modeling of NR2B Modulatory Domain of NMDA Receptor and Analysis of Ifenprodil Binding

ChemMedChem, 2007-10, Vol.2 (10), p.1498-1510

2007

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Theory and applications of the generalized born solvation model in macromolecular simulations

Biopolymers, 2000, Vol.56 (4), p.275-291

2000

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O-Glycoside Orientation Is an Essential Aspect of Base J Recognition by the Kinetoplastid DNA-Binding Protein JBP1

Angewandte Chemie (International ed.), 2007-01, Vol.46 (16), p.2839-2843

2007

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An overview of the Amber biomolecular simulation package

DOCK 6: Impact of new features and current docking performance

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

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

Twenty-five years of nucleic acid simulations

Molecular dynamics simulations of macromolecular crystals

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

Molecular dynamics simulation of triclinic lysozyme in a crystal lattice

Development and testing of a general amber force field

The Amber biomolecular simulation programs

Constant pH molecular dynamics in generalized Born implicit solvent

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

Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures

Molecular dynamics analysis of a flexible loop at the binding interface of the SARS‐CoV‐2 spike protein receptor‐binding domain

Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods

Change in protein flexibility upon complex formation: Analysis of Ras-Raf using molecular dynamics and a molecular framework approach

Exploring protein native states and large-scale conformational changes with a modified generalized born model

Correlated motions in enzymes

Enhanced TROSY Effect in [2‐19F, 2‐13C] Adenosine and ATP Analogs Facilitates NMR Spectroscopy of Very Large Biological RNAs in Solution

New experimental evidence for pervasive dynamics in proteins

Second derivatives in generalized Born theory

Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix

Homology Modeling of NR2B Modulatory Domain of NMDA Receptor and Analysis of Ifenprodil Binding

Theory and applications of the generalized born solvation model in macromolecular simulations

O-Glycoside Orientation Is an Essential Aspect of Base J Recognition by the Kinetoplastid DNA-Binding Protein JBP1

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