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Chemistry

Working Paper

Possibility of HIV-1 Protease Inhibitors-Clinical Trial Drugs as Repurposed Drugs for SARSCoV-2 Main Protease: A Molecular Docking, Molecular Dynamics and Binding Free Energy Simulation Study

Ancy Iruthayaraj, Sivanandam Magudeeswaran, Kumaradhas Poomani

Version 1 posted 28 April 2020

617

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Chemistry

Working Paper

An Approach to Alchemical Binding Free-Energy Calculations Using Coupled Topologies

David Huggins

Version 1 posted 15 October 2018

848

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1

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Chemistry

Working Paper

Drug Repurposing of Allophenylnorstatine Containing HIV-Protease Inhibitors Against SARS-CoV-2 Mpro: Insights from Molecular Dynamics Simulations and Binding Free Energy Estimations

Jiban Jyoti Dash, Priyanka Purohit, Jules Tshishimbi Muya, Biswa Ranjan Meher

Version 1 posted 02 June 2020

742

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1

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Chemistry

Working Paper

Enhancing Paraoxon Binding to Organophosphorus Hydrolase Active Site

Léa El Khoury, David Mobley, Dongmei Ye, Susan Rempe

Version 1 posted 15 February 2021

197

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Chemistry

Working Paper

Optimal Designs of Pairwise Calculation: an Application to Free Energy Perturbation in Minimizing Prediction Variability

Qingyi Yang, Woodrow W. Burchett, Gregory S. Steeno, David L. Mobley, Xinjun Hou

Version 2 posted 02 May 2019

866

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Chemistry

Working Paper

Identification of a Small Molecule that Binds to the PD-L1 Dimer Interface

Wei Xia, Hengwei Bian, Liping He, Suzhen Dong, Yifei Qi, John Z.H. Zhang

Version 1 posted 24 February 2023

170

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Chemistry

Working Paper

Enhancing Sampling of Water Rehydration upon Ligand Binding using Variants of Grand Canonical Monte Carlo

Yunhui Ge, Oliver Melling, Weiming Dong, Jonathan Essex, David Mobley

Version 1 posted 08 August 2022

202

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Chemistry

Working Paper

Predicting the Potential Effect of E484K Mutation on the Binding of 28 Antibodies to the Spike Protein of SARS-CoV-2 by Molecular Dynamics Simulation and Free Energy Calculation

Leyun Wu, Cheng Peng, Zhijian Xu, weiliang zhu

Version 1 posted 11 February 2021

641

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1

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Chemistry

Working Paper

The maximal and current accuracy of rigorous protein-ligand binding free energy calculations

Gregory A Ross, Chao Lu, Guido Scarabelli, Steven K. Albanese, Evelyne Houang, Robert Abel, Edward D. Harder, Lingle Wang

Version 2 posted 13 October 2023

1,332

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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

132

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2

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33 results in binding free energy in Keywords: binding free energy

Possibility of HIV-1 Protease Inhibitors-Clinical Trial Drugs as Repurposed Drugs for SARSCoV-2 Main Protease: A Molecular Docking, Molecular Dynamics and Binding Free Energy Simulation Study

An Approach to Alchemical Binding Free-Energy Calculations Using Coupled Topologies

Drug Repurposing of Allophenylnorstatine Containing HIV-Protease Inhibitors Against SARS-CoV-2 Mpro: Insights from Molecular Dynamics Simulations and Binding Free Energy Estimations

Enhancing Paraoxon Binding to Organophosphorus Hydrolase Active Site

Optimal Designs of Pairwise Calculation: an Application to Free Energy Perturbation in Minimizing Prediction Variability

Identification of a Small Molecule that Binds to the PD-L1 Dimer Interface

Enhancing Sampling of Water Rehydration upon Ligand Binding using Variants of Grand Canonical Monte Carlo

Predicting the Potential Effect of E484K Mutation on the Binding of 28 Antibodies to the Spike Protein of SARS-CoV-2 by Molecular Dynamics Simulation and Free Energy Calculation

The maximal and current accuracy of rigorous protein-ligand binding free energy calculations

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

33 results in Keywords: binding free energy