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8 results in Authors: Bert de Groot

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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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

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

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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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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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

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

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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8 results in Bert de Groot in Authors: Bert de Groot

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

Resolving coupled pH titrations using alchemical free energy calculations

Chemical Space Exploration with Active Learning and Alchemical Free Energies

Alchemical Absolute Protein-Ligand Binding Free Energies for Drug Design

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

Automated relative binding free energy calculations: from SMILES to ΔΔG

Accurately predicting protein pKa values using non-equilibrium alchemy

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

8 results in Authors: Bert de Groot