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Theoretical and Computational Chemistry

Working Paper

Leveraging a separation of states method for relative binding free energy calculations in systems with trapped waters

Swapnil Wagle, Pascal Merz, Yunhui Ge, Christopher Bayly, David Mobley

Version 2 posted 13 November 2024

329

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Theoretical and Computational Chemistry

Working Paper

Reproducibility of Free Energy Calculations Across Different Molecular Simulation Software

Hannes H. Loeffler, Stefano Bosisio, Guilherme Duarte Ramos Matos, Donghyuk Suh, Benoît Roux, David L. Mobley, Julien Michel

Version 1 posted 04 June 2018

982

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Theoretical and Computational Chemistry

Working Paper

A Hybrid Alchemical Free Energy and Machine Learning Methodology for the Calculation of Absolute Hydration Free Energies of Small Molecules

Jenke Scheen, Wilson Wu, Antonia S. J. S. Mey, Paolo Tosco, Mark Mackey, Julien Michel

Version 1 posted 29 May 2020

884

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1

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Theoretical and Computational Chemistry

Working Paper

Blinded Prediction of Protein-Ligand Binding Affinity Using Amber Thermodynamic Integration for the 2018 D3R Grand Challenge 4

Junjie Zou, Chuan Tian, Carlos Simmerling

Version 1 posted 24 June 2019

1,095

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Theoretical and Computational Chemistry

Working Paper

Blinded Predictions of Standard Binding Free Energies: Lessons Learned from the SAMPL6 Challenge

Michail Papadourakis, Stefano Bosisio, Julien Michel

Version 2 posted 16 August 2018

728

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Theoretical and Computational Chemistry

Working Paper

Non-bonded force field parameters from MBIS partitioning of the molecular electron density improve CB7 host-guest affinity predictions

Duvan Gonzalez, Luis Macaya, Carlos Castillo-Orellana, Toon Verstraelen, Stefan Vogt-Geisse, Esteban Vöhringer-Martinez

Version 2 posted 27 May 2022

308

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Theoretical and Computational Chemistry

Working Paper

A Benchmark of Electrostatic Methods Performance in Relative Binding Free Energy Calculations

Yunhui Ge, David F. Hahn, David Mobley

Version 2 posted 16 February 2021

879

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Theoretical and Computational Chemistry

Working Paper

Perturbation Free-Energy Toolkit: Automated Alchemical Topology Builder and Optimized Simulation Update Scheme

Drazen Petrov

Version 1 posted 15 April 2021

544

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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

562

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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

722

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10 results in alchemical free energy calculations in Keywords: alchemical free energy calculations

Leveraging a separation of states method for relative binding free energy calculations in systems with trapped waters

Reproducibility of Free Energy Calculations Across Different Molecular Simulation Software

A Hybrid Alchemical Free Energy and Machine Learning Methodology for the Calculation of Absolute Hydration Free Energies of Small Molecules

Blinded Prediction of Protein-Ligand Binding Affinity Using Amber Thermodynamic Integration for the 2018 D3R Grand Challenge 4

Blinded Predictions of Standard Binding Free Energies: Lessons Learned from the SAMPL6 Challenge

Non-bonded force field parameters from MBIS partitioning of the molecular electron density improve CB7 host-guest affinity predictions

A Benchmark of Electrostatic Methods Performance in Relative Binding Free Energy Calculations

Perturbation Free-Energy Toolkit: Automated Alchemical Topology Builder and Optimized Simulation Update Scheme

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

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

10 results in Keywords: alchemical free energy calculations