Accurate absolute free energies for ligand–protein binding based on non-equilibrium approaches

Molecular dynamics-based approaches to calculate absolute protein–ligand binding free energy often rely on equilibrium free energy perturbation (FEP) protocols. Here, the authors study ligands binding to bromodomains and T4 lysozyme and find that both equilibrium and non-equilibrium approaches conve...

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Autores principales:	Vytautas Gapsys, Ahmet Yildirim, Matteo Aldeghi, Yuriy Khalak, David van der Spoel, Bert L. de Groot
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Chemistry QD1-999
Acceso en línea:	https://doaj.org/article/53ecbf2eedd34149bc3dad8e7658da0f
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spelling	oai:doaj.org-article:53ecbf2eedd34149bc3dad8e7658da0f2021-12-02T17:01:35ZAccurate absolute free energies for ligand–protein binding based on non-equilibrium approaches10.1038/s42004-021-00498-y2399-3669https://doaj.org/article/53ecbf2eedd34149bc3dad8e7658da0f2021-05-01T00:00:00Zhttps://doi.org/10.1038/s42004-021-00498-yhttps://doaj.org/toc/2399-3669Molecular dynamics-based approaches to calculate absolute protein–ligand binding free energy often rely on equilibrium free energy perturbation (FEP) protocols. Here, the authors study ligands binding to bromodomains and T4 lysozyme and find that both equilibrium and non-equilibrium approaches converge to the same results with the non-equilibrium method converging faster than FEP.Vytautas GapsysAhmet YildirimMatteo AldeghiYuriy KhalakDavid van der SpoelBert L. de GrootNature PortfolioarticleChemistryQD1-999ENCommunications Chemistry, Vol 4, Iss 1, Pp 1-13 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Chemistry QD1-999
spellingShingle	Chemistry QD1-999 Vytautas Gapsys Ahmet Yildirim Matteo Aldeghi Yuriy Khalak David van der Spoel Bert L. de Groot Accurate absolute free energies for ligand–protein binding based on non-equilibrium approaches
description	Molecular dynamics-based approaches to calculate absolute protein–ligand binding free energy often rely on equilibrium free energy perturbation (FEP) protocols. Here, the authors study ligands binding to bromodomains and T4 lysozyme and find that both equilibrium and non-equilibrium approaches converge to the same results with the non-equilibrium method converging faster than FEP.
format	article
author	Vytautas Gapsys Ahmet Yildirim Matteo Aldeghi Yuriy Khalak David van der Spoel Bert L. de Groot
author_facet	Vytautas Gapsys Ahmet Yildirim Matteo Aldeghi Yuriy Khalak David van der Spoel Bert L. de Groot
author_sort	Vytautas Gapsys
title	Accurate absolute free energies for ligand–protein binding based on non-equilibrium approaches
title_short	Accurate absolute free energies for ligand–protein binding based on non-equilibrium approaches
title_full	Accurate absolute free energies for ligand–protein binding based on non-equilibrium approaches
title_fullStr	Accurate absolute free energies for ligand–protein binding based on non-equilibrium approaches
title_full_unstemmed	Accurate absolute free energies for ligand–protein binding based on non-equilibrium approaches
title_sort	accurate absolute free energies for ligand–protein binding based on non-equilibrium approaches
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/53ecbf2eedd34149bc3dad8e7658da0f
work_keys_str_mv	AT vytautasgapsys accurateabsolutefreeenergiesforligandproteinbindingbasedonnonequilibriumapproaches AT ahmetyildirim accurateabsolutefreeenergiesforligandproteinbindingbasedonnonequilibriumapproaches AT matteoaldeghi accurateabsolutefreeenergiesforligandproteinbindingbasedonnonequilibriumapproaches AT yuriykhalak accurateabsolutefreeenergiesforligandproteinbindingbasedonnonequilibriumapproaches AT davidvanderspoel accurateabsolutefreeenergiesforligandproteinbindingbasedonnonequilibriumapproaches AT bertldegroot accurateabsolutefreeenergiesforligandproteinbindingbasedonnonequilibriumapproaches
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Accurate absolute free energies for ligand–protein binding based on non-equilibrium approaches

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