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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

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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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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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

932

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2

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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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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

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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Refine Search

20 results in free energy calculation in Keywords: free energy calculation

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

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

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

Modelling of Fibrillation Induced Selective Cytotoxicity of Phenol Soluble Modulin α3

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

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

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

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

20 results in Keywords: free energy calculation