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Theoretical and Computational Chemistry

Working Paper

Relative Binding Free Energy Predictions for Inhibitors of Tetrameric Influenza Virus Neuraminidase

Billy J Williams-Noonan, Elizabeth Yuriev, David K Chalmers

Version 1 posted 14 September 2021

258

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Theoretical and Computational Chemistry

Working Paper

Absolute Binding Free Energy Calculations for Buried Water Molecules

Yunhui Ge, Hannah Baumann, David Mobley

Version 2 posted 29 September 2022

501

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1

Citations

Theoretical and Computational Chemistry

Working Paper

Relative binding free energy between chemically distant compounds using a bidirectional nonequilibrium approach

Piero Procacci

Version 1 posted 22 February 2022

335

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Physical Chemistry

Working Paper

Reliable and Accurate Prediction of Single Residue pKa Values Through Free Energy Perturbation Calculations

Dilek Coskun, Wei Chen, Anthony Clark, Chao Lu, Edward Harder, Lingle Wang, Richard Friesner, Edward Miller

Version 1 posted 21 September 2022

455

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Theoretical and Computational Chemistry

Working Paper

Enhancing Water Sampling in Free Energy Calculations with Grand Canonical Monte Carlo

Gregory Ross, Ellery Russell, Yuqing Deng, Chao Lu, Edward Harder, Robert Abel, Lingle Wang

Version 1 posted 02 July 2020

1,018

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2

Citations

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

677

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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

638

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Theoretical and Computational Chemistry

Working Paper

Q-RepEx: A Python Pipeline to Increase the Sampling of Empirical Valence Bond Simulations

Sebastian Brickel, Andrey O. Demkiv, Rory M. Crean, Gaspar P. Pinto, Shina Caroline Lynn Kamerlin

Version 1 posted 18 November 2022

190

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Theoretical and Computational Chemistry

Working Paper

Induced-Fit Docking Enables Accurate Free Energy Perturbation Calculations in Homology Models

Tianchuan Xu, Kai Zhu, Alexandre Beautrait, Jeremie Vendome, Kenneth Borrelli, Robert Abel, Richard Friesner, Edward Miller

Version 1 posted 15 April 2022

1,030

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3

Citations

Earth, Space, and Environmental Chemistry

Working Paper

Molecular Modelling of Ionic Liquids: Force-Field Validation and Thermodynamic Perspective from Large-Scale Fast-Growth Solvation Free Energy Calculations

Zhaoxi Sun, Mao Wang, Qiaole He, Zhirong Liu

Version 1 posted 03 January 2022

240

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3

Citations

Refine Search

32 results in free energy perturbation in Keywords: free energy perturbation

Relative Binding Free Energy Predictions for Inhibitors of Tetrameric Influenza Virus Neuraminidase

Absolute Binding Free Energy Calculations for Buried Water Molecules

Relative binding free energy between chemically distant compounds using a bidirectional nonequilibrium approach

Reliable and Accurate Prediction of Single Residue pKa Values Through Free Energy Perturbation Calculations

Enhancing Water Sampling in Free Energy Calculations with Grand Canonical Monte Carlo

SAMPL7 TrimerTrip Host-Guest Binding Affinities from Extensive Alchemical and End-Point Free Energy Calculations

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

Q-RepEx: A Python Pipeline to Increase the Sampling of Empirical Valence Bond Simulations

Induced-Fit Docking Enables Accurate Free Energy Perturbation Calculations in Homology Models

Molecular Modelling of Ionic Liquids: Force-Field Validation and Thermodynamic Perspective from Large-Scale Fast-Growth Solvation Free Energy Calculations

32 results in Keywords: free energy perturbation