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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

282

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Theoretical and Computational Chemistry

Working Paper

Accurate Free Energy Calculation via Multiscale Simulations Driven by Hybrid Machine Learning and Molecular Mechanics Potentials

Xujian Wang, Junmei Wang, Xiongwu Wu, Bernard Brooks

Version 1 posted 08 November 2024

293

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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

595

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1

Citations

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

1,810

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2

Citations

Biological and Medicinal Chemistry

Working Paper

Simulating Chalcogen Bonding Using Molecular Mechanics: A Pseudoatom Approach to Model Ebselen.

Thomas Fellowes, JONATHAN WHITE

Version 2 posted 05 May 2021

683

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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

1,602

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Theoretical and Computational Chemistry

Working Paper

Blinded Prediction of Protein-Ligand Binding Affinity Using Amber Thermodynamic Integration for the 2018 D3R Grand Challenge 4

Junjie Zou, Chuan Tian, Carlos Simmerling

Version 1 posted 24 June 2019

1,095

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Theoretical and Computational Chemistry

Working Paper

Exploring Coupled Redox and pH Processes with a Force Field-Based Approach: Applications to Five Different Systems

Vinicius Cruzeiro, Gustavo Troiano Feliciano, Adrian Roitberg

Version 1 posted 03 February 2020

462

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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

178

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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

2,151

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17 results in amber in Keywords: amber

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

Accurate Free Energy Calculation via Multiscale Simulations Driven by Hybrid Machine Learning and Molecular Mechanics Potentials

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

Validation of AMBER/GAFF for Relative Free Energy Calculations

Simulating Chalcogen Bonding Using Molecular Mechanics: A Pseudoatom Approach to Model Ebselen.

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

Blinded Prediction of Protein-Ligand Binding Affinity Using Amber Thermodynamic Integration for the 2018 D3R Grand Challenge 4

Exploring Coupled Redox and pH Processes with a Force Field-Based Approach: Applications to Five Different Systems

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

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

17 results in Keywords: amber