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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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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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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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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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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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Propagated Perturbations from a Peripheral Mutation Show Interactions Supporting WW Domain Thermostability

Structure (London), 2018-11, Vol.26 (11), p.1474-1485.e5

2018

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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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A quantitative model predicts how m6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions

Nature communications, 2021-08, Vol.12 (1), p.5201-5201, Article 5201

2021

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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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Refinement of RNA Structures Using Amber Force Fields

Crystals (Basel), 2021-07, Vol.11 (7), p.771

2021

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Using quantum chemistry to estimate chemical shifts in biomolecules

Biophysical chemistry, 2020-12, Vol.267, p.106476-106476, Article 106476

Case, David A.

2020

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Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate−DNA Helices

Journal of the American Chemical Society, 1998-09, Vol.120 (37), p.9401-9409

1998

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Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions

Journal of chemical theory and computation, 2006-01, Vol.2 (1), p.128-139

2006

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High-Resolution ENDOR Spectroscopy Combined with Quantum Chemical Calculations Reveals the Structure of Nitrogenase Janus Intermediate E4(4H)

Journal of the American Chemical Society, 2019-07, Vol.141 (30), p.11984-11996

2019

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High-Resolution ENDOR Spectroscopy Combined with Quantum Chemical Calculations Reveals the Structure of Nitrogenase Janus Intermediate E 4 (4H)

Journal of the American Chemical Society, 2019-07, Vol.141 (30), p.11984-11996

2019

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RNA Electrostatics: How Ribozymes Engineer Active Sites to Enable Catalysis

The journal of physical chemistry. B, 2022-08, Vol.126 (32), p.5982-5990

2022

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Correlated motions in enzymes

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

2022

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Classical molecular dynamics

The Journal of chemical physics, 2021-03, Vol.154 (10), p.100401-100401

2021

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AmberTools

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

2023

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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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AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules

Computer physics communications, 1995-01, Vol.91 (1), p.1-41

1995

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Reconciling Structural and Spectroscopic Fingerprints of the Oxygen-Evolving Complex of Photosystem II: A Computational Study of the S 2 State

The journal of physical chemistry. B, 2018-12, Vol.122 (50), p.11868-11882

2018

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Proton Binding to Proteins: pKa Calculations with Explicit and Implicit Solvent Models

Journal of the American Chemical Society, 2004-04, Vol.126 (13), p.4167-4180

2004

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An overview of the Amber biomolecular simulation package

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

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

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

Structure of the HIV-1 RNA packaging signal

Molecular dynamics simulations of macromolecular crystals

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

Propagated Perturbations from a Peripheral Mutation Show Interactions Supporting WW Domain Thermostability

Modification of the Generalized Born Model Suitable for Macromolecules

A quantitative model predicts how m6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions

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

Refinement of RNA Structures Using Amber Force Fields

Using quantum chemistry to estimate chemical shifts in biomolecules

Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate−DNA Helices

Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions

High-Resolution ENDOR Spectroscopy Combined with Quantum Chemical Calculations Reveals the Structure of Nitrogenase Janus Intermediate E4(4H)

High-Resolution ENDOR Spectroscopy Combined with Quantum Chemical Calculations Reveals the Structure of Nitrogenase Janus Intermediate E 4 (4H)

RNA Electrostatics: How Ribozymes Engineer Active Sites to Enable Catalysis

Correlated motions in enzymes

Classical molecular dynamics

AmberTools

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

AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules

Reconciling Structural and Spectroscopic Fingerprints of the Oxygen-Evolving Complex of Photosystem II: A Computational Study of the S 2 State

Proton Binding to Proteins: pKa Calculations with Explicit and Implicit Solvent Models

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