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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

860

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1

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Biological and Medicinal Chemistry

Working Paper

How Reactive are Druggable Cysteines in Protein Kinases?

Ernest Awoonor-Williams, Christopher Rowley

Version 1 posted 10 October 2017

1,182

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Theoretical and Computational Chemistry

Working Paper

Insights on Small Molecule Binding to the Hv1 Proton Channel from Free Energy Calculations with Molecular Dynamics Simulations

Victoria T. Lim, Andrew D. Geragotelis, Nathan M. Lim, J. Alfredo Freites, Francesco Tombola, David Mobley, Doug Tobias

Version 1 posted 06 February 2020

553

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Physical Chemistry

Working Paper

Determination of Base Flipping Free Energy Landscapes from Nonequilibrium Stratification

Xiaohui Wang, Zhaoxi Sun

Version 2 posted 21 March 2019

1,141

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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

881

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Biological and Medicinal Chemistry

Working Paper

A Free Energy Perturbation Approach to Estimate the Intrinsic Solubilities of Drug-like Small Molecules

Sayan Mondal, Gary Tresadern, Jeremy Greenwood, Byungchan Kim, Joe Kaus, Matt Wirtala, Thomas Steinbrecher, Lingle Wang, Craig Masse, Ramy Farid, Robert Abel

Version 1 posted 15 November 2019

2,258

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4

Citations

Biological and Medicinal Chemistry

Working Paper

Disruption of water networks is the cause of human/mouse species selectivity in urokinase plasminogen activator (uPA) inhibitors derived from hexamethylene amiloride (HMA)

Nehad El Salamouni, Benjamin Buckley, Longguang Jiang, Mingdong Huang, Marie Ranson, Michael Kelso, Haibo Yu

Version 3 posted 04 October 2021

606

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Theoretical and Computational Chemistry

Working Paper

Seeding the Multi-dimensional Nonequilibrium Pulling for Hamiltonian Variation: Indirect Nonequilibrium Free Energy Simulations at QM levels

Zhaoxi Sun, Qiaole He

Version 2 posted 04 October 2021

412

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Physical Chemistry

Working Paper

BAR-Based Multi-dimensional Nonequilibrium Pulling for Indirect Construction of QM/MM Free Energy Landscape: From Semi-Empirical to Ab Initio

Zhaoxi Sun

Version 2 posted 23 September 2019

721

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Biological and Medicinal Chemistry

Working Paper

Computational Determination of Potential Inhibitors of SARS-CoV-2 Main Protease

Son Tung Ngo, Ngoc Quynh Anh Pham, Ly Le, Duc-Hung Pham, Van Vu

Version 2 posted 02 June 2020

1,465

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32 results in Free Energy Perturbation in Keywords: Free Energy Perturbation

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

How Reactive are Druggable Cysteines in Protein Kinases?

Insights on Small Molecule Binding to the Hv1 Proton Channel from Free Energy Calculations with Molecular Dynamics Simulations

Determination of Base Flipping Free Energy Landscapes from Nonequilibrium Stratification

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

A Free Energy Perturbation Approach to Estimate the Intrinsic Solubilities of Drug-like Small Molecules

Disruption of water networks is the cause of human/mouse species selectivity in urokinase plasminogen activator (uPA) inhibitors derived from hexamethylene amiloride (HMA)

Seeding the Multi-dimensional Nonequilibrium Pulling for Hamiltonian Variation: Indirect Nonequilibrium Free Energy Simulations at QM levels

BAR-Based Multi-dimensional Nonequilibrium Pulling for Indirect Construction of QM/MM Free Energy Landscape: From Semi-Empirical to Ab Initio

Computational Determination of Potential Inhibitors of SARS-CoV-2 Main Protease

32 results in Keywords: Free Energy Perturbation