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Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes Using Nonequilibrium Candidate Monte Carlo

Samuel Gill, Nathan M. Lim, Patrick Grinaway, Ariën S. Rustenburg, Josh Fass, Gregory Ross, John D. Chodera, David Mobley

Version 5 posted 23 February 2018

3,501

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Theoretical and Computational Chemistry

Working Paper

Bind3P: Optimization of a Water Model with Host-Guest Binding Data

Jian Yin, Niel M. Henriksen, Hari S. Muddana, Michael K. Gilson

Version 2 posted 02 April 2018

1,032

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Biological and Medicinal 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

689

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Theoretical and Computational Chemistry

Working Paper

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

David Huggins

Version 1 posted 15 October 2018

887

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1

Citations

Biological and Medicinal 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

819

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Theoretical and Computational 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

934

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Physical 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

230

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Physical Chemistry

Working Paper

Thermodynamics and Kinetics in Antibody Resistance of the 501Y.V2 SARS-CoV-2 Variant

Son Tung Ngo, Trung Hai Nguyen, Duc-Hung Pham, Nguyen Thanh Tung, Pham Cam Nam

Version 4 posted 18 May 2021

802

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1

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Theoretical and Computational Chemistry

Working Paper

Membrane Permeation of Psychedelic Compounds

Vito Federico Palmisano, Claudio Agnorelli, Andrea Fagiolini, David Erritzoe, David Nutt, Shirin Faraji, Juan Jose Nogueira

Version 1 posted 31 October 2023

255

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Theoretical and Computational Chemistry

Working Paper

Identification of Potential Molecules Against COVID-19 Main Protease Through Structure-Guided Virtual Screening Approach

Lovika Mittal, Anita Kumari, Mitul Srivastava, Mrityunjay Singh, Shailendra Asthana

Version 2 posted 10 April 2020

1,938

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5

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Refine Search

38 results in Binding Free Energy in Keywords: Binding Free Energy

Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes Using Nonequilibrium Candidate Monte Carlo

Bind3P: Optimization of a Water Model with Host-Guest Binding Data

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

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

Enhancing Paraoxon Binding to Organophosphorus Hydrolase Active Site

Thermodynamics and Kinetics in Antibody Resistance of the 501Y.V2 SARS-CoV-2 Variant

Membrane Permeation of Psychedelic Compounds

Identification of Potential Molecules Against COVID-19 Main Protease Through Structure-Guided Virtual Screening Approach

38 results in Keywords: Binding Free Energy