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Theoretical and Computational Chemistry

Working Paper

Comparison of Receptor-Ligand Restraint Schemes for Alchemical Absolute Binding Free Energy Calculations

Finlay Clark, Graeme Robb, Daniel Cole, Julien Michel

Version 2 posted 09 May 2023

547

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Theoretical and Computational Chemistry

Review

Sire: An Interoperability Engine for Prototyping Algorithms and Exchanging Information Between Molecular Simulation Programs

Christopher Woods, Lester Hedges, Adrian Mulholland, Maturos Malaisree, Paolo Tosco, Hannes Loeffler, Miroslav Suruzhon, Matthew Burman, Sofia Bariami, Stefano Bosisio, Gaetano Calabro, Finlay Clark, Antonia Mey, Julien Michel

Version 1 posted 30 January 2024

149

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Physical Chemistry

Working Paper

Konnektor: A framework for using graph theory to plan networks for free energy calculations

Benjamin Ries, Richard J Gowers, James RB Eastwood, Irfan Alibay, Hannah M Baumann, David WH Swenson, Michael M Henry, David Mobley

Version 1 posted 12 September 2024

258

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Theoretical and Computational Chemistry

Working Paper

BAT2: An open-source tool for flexible, automated and low cost absolute binding free energy calculations

Germano Heinzelmann, David Huggins, Michael Gilson

Version 2 posted 22 February 2024

898

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Earth, Space, and Environmental Chemistry

Working Paper

Determining the Complete Stability of Calcite Kink Sites: Real vs Ideal

Blake Armstrong, Alessandro Silvestri, Marco De La Pierre, Paolo Raiteri, Julian Gale

Version 2 posted 29 June 2023

242

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Theoretical and Computational Chemistry

Working Paper

Reweighting from Molecular Mechanics Force Fields to the ANI-2x Neural Network Potential

Sara Tkaczyk, Johannes Karwounopoulos, Andreas Schöller, H. Lee Woodcock, Thierry Langer, Stefan Boresch, Marcus Wieder

Version 3 posted 19 March 2024

1,087

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Theoretical and Computational Chemistry

Working Paper

Kartograf: An Accurate Geometry-Based Atom Mapper for Hybrid Topology Relative Free Energy Calculations

Benjamin Ries, Irfan Alibay, David W H Swenson, Hannah M Baumann, Michael M Henry, James RB Eastwood, Richard J Gowers

Version 1 posted 31 October 2023

313

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Materials Science

Working Paper

Large-Scale Free Energy Calculations on a Computational MOF Database: Toward Synthetic Likelihood Predictions

Ryther Anderson, Diego Gómez-Gualdrón

Version 1 posted 21 February 2020

788

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1

Citations

Theoretical and Computational Chemistry

Working Paper

Partition Coefficients of Methylated DNA Bases Obtained from Free Energy Calculations with Molecular Electron Density Derived Atomic Charges.

Alejandro Lara, Maximiliano Riquelme, Esteban Vöhringer-Martinez

Version 1 posted 17 January 2018

487

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Theoretical and Computational Chemistry

Working Paper

Elucidating Biophysical Basis of Binding of Inhibitors to SARS-CoV-2 Main Protease by Using Molecular Dynamics Simulations and Free Energy Calculations

Md Fulbabu Sk, Rajarshi Roy, Nisha Amarnath Jonniya, Sayan Poddar, Parimal Kar

Version 1 posted 06 April 2020

1,122

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49 results in Free energy calculations in Keywords: Free energy calculations

Comparison of Receptor-Ligand Restraint Schemes for Alchemical Absolute Binding Free Energy Calculations

Sire: An Interoperability Engine for Prototyping Algorithms and Exchanging Information Between Molecular Simulation Programs

Konnektor: A framework for using graph theory to plan networks for free energy calculations

BAT2: An open-source tool for flexible, automated and low cost absolute binding free energy calculations

Determining the Complete Stability of Calcite Kink Sites: Real vs Ideal

Reweighting from Molecular Mechanics Force Fields to the ANI-2x Neural Network Potential

Kartograf: An Accurate Geometry-Based Atom Mapper for Hybrid Topology Relative Free Energy Calculations

Large-Scale Free Energy Calculations on a Computational MOF Database: Toward Synthetic Likelihood Predictions

Partition Coefficients of Methylated DNA Bases Obtained from Free Energy Calculations with Molecular Electron Density Derived Atomic Charges.

Elucidating Biophysical Basis of Binding of Inhibitors to SARS-CoV-2 Main Protease by Using Molecular Dynamics Simulations and Free Energy Calculations

49 results in Keywords: Free energy calculations