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10 results in Authors: Vytautas Gapsys

Development and Benchmarking of Open Force Field 2.0.0 — the Sage Small Molecule Force Field

Simon Boothroyd, Pavan Kumar Behara, Owen Madin, David Hahn, Hyesu Jang, Vytautas Gapsys, Jeffrey Wagner, Joshua Horton, David Dotson, Matthew Thompson, Jessica Maat, Trevor Gokey, Lee-Ping Wang, Daniel Cole, Michael Gilson, John Chodera, Christopher Bayly, Michael Shirts, David Mobley

Version 2 posted 10 January 2023

1,467

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Theoretical and Computational Chemistry

Working Paper

Cysteine and histidine pKa prediction: alchemical free energy calculations and force field reparameterization

Carter J. Wilson, Vytautas Gapsys, Bert L. de Groot

Version 1 posted 18 October 2024

152

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Theoretical and Computational Chemistry

Working Paper

Current state of open source force fields in protein-ligand binding affinity predictions

David F. Hahn, Vytautas Gapsys, Bert L. de Groot, David L. Mobley, Gary J. Tresadern

Version 1 posted 29 August 2023

1,853

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Citations

Theoretical and Computational Chemistry

Working Paper

Chemical Space Exploration with Active Learning and Alchemical Free Energies

Yuriy Khalak, Gary Tresadern, David F. Hahn, Bert L. de Groot, Vytautas Gapsys

Version 1 posted 13 July 2022

512

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Theoretical and Computational Chemistry

Working Paper

Broadening the scope of binding free energy calculations using a Separated Topologies approach

Hannah M. Baumann, Eric Dybeck, Christopher Lee McClendon, Frank C. Pickard IV, Vytautas Gapsys, Laura Pérez-Benito, David F. Hahn, Gary Tresadern, Alan M. Mathiowetz, David L. Mobley

Version 1 posted 10 March 2023

932

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Theoretical and Computational Chemistry

Working Paper

Alchemical Absolute Protein-Ligand Binding Free Energies for Drug Design

Yuriy Khalak, Gary Tresadern, Matteo Aldeghi, Hannah Magdalena Baumann, David L. Mobley, Bert L. de Groot, Vytautas Gapsys

Version 2 posted 27 September 2021

1,426

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Biological and Medicinal Chemistry

Working Paper

Automated relative binding free energy calculations: from SMILES to ΔΔG

Harry Moore, Christian Margreitter, Jon Paul Janet, Ola Engkvist, Bert de Groot, Vytautas Gapsys

Version 1 posted 25 August 2022

1,271

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Theoretical and Computational Chemistry

Working Paper

Resolving coupled pH titrations using alchemical free energy calculations

Carter J. Wilson, Bert L. de Groot, Vytautas Gapsys

Version 3 posted 07 November 2023

528

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Theoretical and Computational Chemistry

Working Paper

Accurately predicting protein pKa values using non-equilibrium alchemy

Carter J. Wilson, Mikko Karttunen, Bert L. de Groot, Vytautas Gapsys

Version 2 posted 29 June 2023

530

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Theoretical and Computational Chemistry

Working Paper

Challenges Encountered Applying Equilibrium and Non-Equilibrium Binding Free Energy Calculations

Hannah Baumann, Vytautas Gapsys, Bert L. de Groot, David Mobley

Version 2 posted 13 April 2021

1,165

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10 results in Vytautas Gapsys in Authors: Vytautas Gapsys

Development and Benchmarking of Open Force Field 2.0.0 — the Sage Small Molecule Force Field

Cysteine and histidine pKa prediction: alchemical free energy calculations and force field reparameterization

Current state of open source force fields in protein-ligand binding affinity predictions

Chemical Space Exploration with Active Learning and Alchemical Free Energies

Broadening the scope of binding free energy calculations using a Separated Topologies approach

Alchemical Absolute Protein-Ligand Binding Free Energies for Drug Design

Automated relative binding free energy calculations: from SMILES to ΔΔG

Resolving coupled pH titrations using alchemical free energy calculations

Accurately predicting protein pKa values using non-equilibrium alchemy

Challenges Encountered Applying Equilibrium and Non-Equilibrium Binding Free Energy Calculations

10 results in Authors: Vytautas Gapsys