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Theoretical and Computational Chemistry

Working Paper

Enhancing Water Sampling in Free Energy Calculations with Grand Canonical Monte Carlo

Gregory Ross, Ellery Russell, Yuqing Deng, Chao Lu, Edward Harder, Robert Abel, Lingle Wang

Version 1 posted 02 July 2020

1,153

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2

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Physical Chemistry

Working Paper

Determination of Base Flipping Free Energy Landscapes from Nonequilibrium Stratification

Xiaohui Wang, Zhaoxi Sun

Version 2 posted 21 March 2019

1,180

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Theoretical and Computational Chemistry

Working Paper

An Approach to Alchemical Binding Free-Energy Calculations Using Coupled Topologies

David Huggins

Version 1 posted 15 October 2018

887

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1

Citations

Physical Chemistry

Working Paper

BAR-based Multi-dimensional Nonequilibrium Pulling for Indirect Construction of QM/MM Free Energy Landscapes: Varying the QM Region

Zhaoxi Sun, Zhirong Liu

Version 3 posted 30 March 2021

498

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Biological and Medicinal Chemistry

Working Paper

How Reactive are Druggable Cysteines in Protein Kinases?

Ernest Awoonor-Williams, Christopher Rowley

Version 1 posted 10 October 2017

1,200

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Physical Chemistry

Working Paper

BAR-Based Multi-dimensional Nonequilibrium Pulling for Indirect Construction of QM/MM Free Energy Landscape: From Semi-Empirical to Ab Initio

Zhaoxi Sun

Version 2 posted 23 September 2019

740

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Theoretical and Computational Chemistry

Working Paper

Seeding the Multi-dimensional Nonequilibrium Pulling for Hamiltonian Variation: Indirect Nonequilibrium Free Energy Simulations at QM levels

Zhaoxi Sun, Qiaole He

Version 2 posted 04 October 2021

455

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Physical Chemistry

Working Paper

Theoretical Understanding of the Thermodynamics and Interactions in Transcriptional Regulator TtgR-Ligand Binding

Zhaoxi Sun, Xiaohui Wang, John Z. H. Zhang

Version 1 posted 15 July 2019

676

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Theoretical and Computational Chemistry

Working Paper

The maximal and current accuracy of rigorous protein-ligand binding free energy calculations

Gregory A Ross, Chao Lu, Guido Scarabelli, Steven K. Albanese, Evelyne Houang, Robert Abel, Edward D. Harder, Lingle Wang

Version 2 posted 13 October 2023

1,780

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Theoretical and Computational Chemistry

Working Paper

Induced-Fit Docking Enables Accurate Free Energy Perturbation Calculations in Homology Models

Tianchuan Xu, Kai Zhu, Alexandre Beautrait, Jeremie Vendome, Kenneth Borrelli, Robert Abel, Richard Friesner, Edward Miller

Version 1 posted 15 April 2022

1,178

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3

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Refine Search

37 results in Free energy perturbation in Keywords: Free energy perturbation

Enhancing Water Sampling in Free Energy Calculations with Grand Canonical Monte Carlo

Determination of Base Flipping Free Energy Landscapes from Nonequilibrium Stratification

An Approach to Alchemical Binding Free-Energy Calculations Using Coupled Topologies

BAR-based Multi-dimensional Nonequilibrium Pulling for Indirect Construction of QM/MM Free Energy Landscapes: Varying the QM Region

How Reactive are Druggable Cysteines in Protein Kinases?

BAR-Based Multi-dimensional Nonequilibrium Pulling for Indirect Construction of QM/MM Free Energy Landscape: From Semi-Empirical to Ab Initio

Seeding the Multi-dimensional Nonequilibrium Pulling for Hamiltonian Variation: Indirect Nonequilibrium Free Energy Simulations at QM levels

Theoretical Understanding of the Thermodynamics and Interactions in Transcriptional Regulator TtgR-Ligand Binding

The maximal and current accuracy of rigorous protein-ligand binding free energy calculations

Induced-Fit Docking Enables Accurate Free Energy Perturbation Calculations in Homology Models

37 results in Keywords: Free energy perturbation