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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

473

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Physical Chemistry

Working Paper

SAMPL7 TrimerTrip Host-Guest Binding Affinities from Extensive Alchemical and End-Point Free Energy Calculations

Zhe Huai, Huaiyu Yang, Xiao Li, Zhaoxi Sun

Version 2 posted 29 September 2020

677

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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

352

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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

170

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2

Citations

Earth, Space, and Environmental Chemistry

Working Paper

Molecular Modelling of Ionic Liquids: Force-Field Validation and Thermodynamic Perspective from Large-Scale Fast-Growth Solvation Free Energy Calculations

Zhaoxi Sun, Mao Wang, Qiaole He, Zhirong Liu

Version 1 posted 03 January 2022

240

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3

Citations

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

384

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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

172

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Theoretical and Computational Chemistry

Working Paper

Broadening the scope of binding free energy calculations using a Separated Topologies approach

Hannah M. Baumann, Eric Dybeck, Christopher Lee McClendon, Frank C. Pickard IV, Vytautas Gapsys, Laura Pérez-Benito, David F. Hahn, Gary Tresadern, Alan M. Mathiowetz, David L. Mobley

Version 1 posted 10 March 2023

844

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2

Citations

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

638

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Biological and Medicinal Chemistry

Working Paper

Modelling of Fibrillation Induced Selective Cytotoxicity of Phenol Soluble Modulin α3

Mitradip Das, Sandeep Dash, B. L. Bhargava

Version 1 posted 21 January 2019

636

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Refine Search

18 results in Free energy calculation in Keywords: Free energy calculation

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

SAMPL7 TrimerTrip Host-Guest Binding Affinities from Extensive Alchemical and End-Point Free Energy Calculations

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

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

Molecular Modelling of Ionic Liquids: Force-Field Validation and Thermodynamic Perspective from Large-Scale Fast-Growth Solvation Free Energy Calculations

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

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

Broadening the scope of binding free energy calculations using a Separated Topologies approach

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

Modelling of Fibrillation Induced Selective Cytotoxicity of Phenol Soluble Modulin α3

18 results in Keywords: Free energy calculation