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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

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

164

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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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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

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

175

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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

385

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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

348

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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

181

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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

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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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Refine Search

18 results in Free Energy Calculation in Keywords: Free Energy Calculation

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

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

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

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

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

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

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

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

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

18 results in Keywords: Free Energy Calculation