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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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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

648

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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

722

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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

391

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Theoretical and Computational Chemistry

Working Paper

Uni-GBSA: An Automatic Workflow to Perform MM/GB(PB)SA Calculations for Virtual Screening

Maohua Yang, Dongdong Wang, Hang Zheng

Version 1 posted 29 September 2022

514

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1

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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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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

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

193

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3

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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

414

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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

194

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20 results in Free Energy Calculation in Keywords: Free Energy Calculation

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

Modelling of Fibrillation Induced Selective Cytotoxicity of Phenol Soluble Modulin α3

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

Uni-GBSA: An Automatic Workflow to Perform MM/GB(PB)SA Calculations for Virtual Screening

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

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: III. Force-Field Comparison, Three-Trajectory Realization and Further Dielectric Augmentation

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

20 results in Keywords: Free Energy Calculation