Search

Biological and Medicinal Chemistry

Working Paper

Thermodynamic and structural insights into the repurposing of drugs that bind to SARS-CoV-2 main protease

Shunzhou Wan, Agastya Bhati, Alexander Wade, Dario Alfe, Peter Coveney

Version 2 posted 30 August 2021

371

Downloads

Theoretical and Computational Chemistry

Working Paper

Comprehensive Evaluation of End-Point Free Energy Techniques in Carboxylated-Pillar[6]arene Host-guest Binding: III. Force-Field Comparison, Three-Trajectory Realization and Further Dielectric Augmentation

Xiao Liu, Lei Zheng, Chu Qin, Yalong Cong, John Z. H. Zhang, Zhaoxi Sun

Version 1 posted 27 February 2023

184

Downloads

2

Citations

Theoretical and Computational Chemistry

Working Paper

Principled Approach for Computing Free Energy on Perturbation Graphs with Cycles

Xinqiang Ding, John Drohan

Version 1 posted 22 July 2024

97

Downloads

Theoretical and Computational Chemistry

Working Paper

Multistate Method to Efficiently Account for Tautomerism and Protonation in Alchemical Free-Energy Calculations

Candide Champion, Philippe H. Hünenberger, Sereina Riniker

Version 1 posted 26 March 2024

228

Downloads

Theoretical and Computational Chemistry

Working Paper

Current state of open source force fields in protein-ligand binding affinity predictions

David F. Hahn, Vytautas Gapsys, Bert L. de Groot, David L. Mobley, Gary J. Tresadern

Version 1 posted 29 August 2023

1,799

Downloads

2

Citations

Biological and Medicinal Chemistry

Working Paper

Comprehensive Evaluation of End-Point Free Energy Techniques in Carboxylated-Pillar[6]arene Host-guest Binding: II. Regression and Dielectric Constant

Xiao Liu, Lei Zheng, Yalong Cong, Zhihao Gong, Zhixiang Yin, John Zhang, Zhirong Liu, Zhaoxi Sun

Version 1 posted 26 August 2022

196

Downloads

Theoretical and Computational Chemistry

Working Paper

Which corners to cut? Guidelines on choosing optimal settings to maximise sampling with limited computational resources

Peter V. Coveney, Shunzhou Wan, Agastya P. Bhati, Alexander D. Wade

Version 1 posted 05 August 2022

186

Downloads

2

Citations

Theoretical and Computational Chemistry

Working Paper

The performance of ensemble-based free energy protocols in computing binding affinities to ROS1 kinase

Shunzhou Wan, Agastya P. Bhati, David W. Wright, Alexander D. Wade, Gary Tresadern, Herman van Vlijmen, Peter V. Coveney

Version 1 posted 14 March 2022

189

Downloads

Physical Chemistry

Working Paper

EPISOL: A Software Package with Expanded Functions to Perform 3D-RISM Calculations for the Solvation of Chemical and Biological Molecules

Siqin Cao, Michael Kalin, Xuhui Huang

Version 1 posted 31 October 2022

394

Downloads

Theoretical and Computational Chemistry

Working Paper

Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases

Candide Champion, René Gall, Benjamin Ries, Salomé R. Rieder, Emilia P. Barros, Sereina Riniker

Version 2 posted 14 September 2023

378

Downloads

Refine Search

19 results in free energy calculation in Keywords: free energy calculation

Thermodynamic and structural insights into the repurposing of drugs that bind to SARS-CoV-2 main protease

Comprehensive Evaluation of End-Point Free Energy Techniques in Carboxylated-Pillar[6]arene Host-guest Binding: III. Force-Field Comparison, Three-Trajectory Realization and Further Dielectric Augmentation

Principled Approach for Computing Free Energy on Perturbation Graphs with Cycles

Multistate Method to Efficiently Account for Tautomerism and Protonation in Alchemical Free-Energy Calculations

Current state of open source force fields in protein-ligand binding affinity predictions

Comprehensive Evaluation of End-Point Free Energy Techniques in Carboxylated-Pillar[6]arene Host-guest Binding: II. Regression and Dielectric Constant

Which corners to cut? Guidelines on choosing optimal settings to maximise sampling with limited computational resources

The performance of ensemble-based free energy protocols in computing binding affinities to ROS1 kinase

EPISOL: A Software Package with Expanded Functions to Perform 3D-RISM Calculations for the Solvation of Chemical and Biological Molecules

Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases

19 results in Keywords: free energy calculation