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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

Principled Approach for Computing Free Energy on Perturbation Graphs with Cycles

Xinqiang Ding, John Drohan

Version 1 posted 22 July 2024

141

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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

390

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Catalysis

Working Paper

Melamine-driven solvation effect promotes oxygen reduction on platinum catalyst: machine learning-aided free energy calculations

Ryosuke Jinnouchi, Saori Minami

Version 1 posted 15 October 2024

106

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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

239

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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

1,853

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2

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Biological and Medicinal Chemistry

Working Paper

Allosteric Modulation of PCSK9-LDLR Interaction: Can Structureless Loops be Drug Targets?

Ipsita Basu, Krishnendu Sinha, Zacharia Shah, Salim Shah, Suman Chakrabarty

Version 1 posted 31 October 2022

439

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Theoretical and Computational Chemistry

Working Paper

Hybrid QM/MM free energy evaluation of drug-resistant mutational effect on binding of an inhibitor Indinavir to HIV-1 protease

Masahiko Taguchi, Ryo Oyama, Masahiro Kaneso, Shigehiko Hayashi

Version 5 posted 25 February 2022

623

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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

193

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2

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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

193

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3

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Refine Search

20 results in Free energy calculation in Keywords: Free energy calculation

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

Principled Approach for Computing Free Energy on Perturbation Graphs with Cycles

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

Melamine-driven solvation effect promotes oxygen reduction on platinum catalyst: machine learning-aided free energy calculations

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

Allosteric Modulation of PCSK9-LDLR Interaction: Can Structureless Loops be Drug Targets?

Hybrid QM/MM free energy evaluation of drug-resistant mutational effect on binding of an inhibitor Indinavir to HIV-1 protease

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

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

20 results in Keywords: Free energy calculation