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Theoretical and Computational Chemistry

Working Paper

Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations

Ido Ben-Shalom, Zhixiong Lin, Brian Radak, Charles Lin, Woody Sherman, Michael K. Gilson

Version 1 posted 20 July 2020

592

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1

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Biological and Medicinal Chemistry

Working Paper

A Fast Implementation of the Nudged Elastic Band Method in AMBER

Delaram Ghoreishi, David Cerutti, Zachary Fallon, Carlos Simmerling, Adrian Roitberg

Version 1 posted 18 June 2019

807

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Theoretical and Computational Chemistry

Working Paper

Systematic comparison of Amber and Rosetta energy functions for protein structure evaluation.

Aliza Rubenstein, Kristin Blacklock, Hai Nguyen, David Case, Sagar Khare

Version 2 posted 04 April 2018

1,572

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Theoretical and Computational Chemistry

Working Paper

ff19SB: Amino-Acid Specific Protein Backbone Parameters Trained Against Quantum Mechanics Energy Surfaces in Solution

Chuan Tian, Koushik Kasavajhala, Kellon Belfon, Lauren Raguette, He Huang, Angela Migues, John Bickel, Yuzhang Wang, Jorge Pincay, Qin Wu, Carlos Simmerling

Version 1 posted 17 June 2019

2,603

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1

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Theoretical and Computational Chemistry

Working Paper

Validation of AMBER/GAFF for Relative Free Energy Calculations

Lin Song, Tai-Sung Lee, Chun Zhu, Darrin M. York, Kenneth M. Merz Jr.

Version 1 posted 04 February 2019

1,792

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2

Citations

Theoretical and Computational Chemistry

Working Paper

Open-Source Multi-GPU-Accelerated QM/MM Simulations with AMBER and QUICK

Vinicius Cruzeiro, Madushanka Manathunga, Kenneth M. Merz, Jr., Andreas Goetz

Version 1 posted 16 February 2021

2,077

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Theoretical and Computational Chemistry

Working Paper

QM/MM Simulations on NVIDIA and AMD GPUs

Madushanka Manathunga, Hasan Metin Aktulga, Andreas W. Goetz, Kenneth M. Merz, Jr

Version 1 posted 30 November 2022

464

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Chemical Engineering and Industrial Chemistry

Working Paper

Molecular Modelling of Ionic Liquids: General Guidelines on Fixed-Charge Force Fields for Balanced Descriptions

Zhaoxi Sun, Zhihao Gong, Lei Zheng, Payam Kalhor, Zhe Huai, Zhirong Liu

Version 2 posted 30 June 2022

494

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Theoretical and Computational Chemistry

Working Paper

Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy)Ribose…Nucleobase Lone-pair…π Contacts in Nucleic Acids.

Klaudia Mrazikova, Jiri Sponer, Vojtech Mlynsky, Pascal Auffinger, Holger Kruse

Version 1 posted 15 September 2021

278

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Theoretical and Computational Chemistry

Working Paper

Influence of non-protein amino-acid mimosine in peptide conformational propensities from novel Amber force field parameters

Asier Urriolabeitia, David De Sancho, Xabier López

Version 1 posted 09 November 2021

170

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16 results in amber in Keywords: amber

Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations

A Fast Implementation of the Nudged Elastic Band Method in AMBER

Systematic comparison of Amber and Rosetta energy functions for protein structure evaluation.

ff19SB: Amino-Acid Specific Protein Backbone Parameters Trained Against Quantum Mechanics Energy Surfaces in Solution

Validation of AMBER/GAFF for Relative Free Energy Calculations

Open-Source Multi-GPU-Accelerated QM/MM Simulations with AMBER and QUICK

QM/MM Simulations on NVIDIA and AMD GPUs

Molecular Modelling of Ionic Liquids: General Guidelines on Fixed-Charge Force Fields for Balanced Descriptions

Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy)Ribose…Nucleobase Lone-pair…π Contacts in Nucleic Acids.

Influence of non-protein amino-acid mimosine in peptide conformational propensities from novel Amber force field parameters

16 results in Keywords: amber