Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design

[Image: see text] Nowadays, drug design projects benefit from highly accurate protein–ligand binding free energy predictions based on molecular dynamics simulations. While such calculations have been computationally expensive in the past, we now demonstrate that workflows built on open source softwa...

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Autores principales: Gapsys, Vytautas, Hahn, David F., Tresadern, Gary, Mobley, David L., Rampp, Markus, de Groot, Bert L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2022
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8924919/
https://www.ncbi.nlm.nih.gov/pubmed/35191702
http://dx.doi.org/10.1021/acs.jcim.1c01445
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author Gapsys, Vytautas
Hahn, David F.
Tresadern, Gary
Mobley, David L.
Rampp, Markus
de Groot, Bert L.
author_facet Gapsys, Vytautas
Hahn, David F.
Tresadern, Gary
Mobley, David L.
Rampp, Markus
de Groot, Bert L.
author_sort Gapsys, Vytautas
collection PubMed
description [Image: see text] Nowadays, drug design projects benefit from highly accurate protein–ligand binding free energy predictions based on molecular dynamics simulations. While such calculations have been computationally expensive in the past, we now demonstrate that workflows built on open source software packages can efficiently leverage pre-exascale computing resources to screen hundreds of compounds in a matter of days. We report our results of free energy calculations on a large set of pharmaceutically relevant targets assembled to reflect industrial drug discovery projects.
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spelling pubmed-89249192022-03-17 Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design Gapsys, Vytautas Hahn, David F. Tresadern, Gary Mobley, David L. Rampp, Markus de Groot, Bert L. J Chem Inf Model [Image: see text] Nowadays, drug design projects benefit from highly accurate protein–ligand binding free energy predictions based on molecular dynamics simulations. While such calculations have been computationally expensive in the past, we now demonstrate that workflows built on open source software packages can efficiently leverage pre-exascale computing resources to screen hundreds of compounds in a matter of days. We report our results of free energy calculations on a large set of pharmaceutically relevant targets assembled to reflect industrial drug discovery projects. American Chemical Society 2022-02-22 2022-03-14 /pmc/articles/PMC8924919/ /pubmed/35191702 http://dx.doi.org/10.1021/acs.jcim.1c01445 Text en © 2022 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Gapsys, Vytautas
Hahn, David F.
Tresadern, Gary
Mobley, David L.
Rampp, Markus
de Groot, Bert L.
Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design
title Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design
title_full Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design
title_fullStr Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design
title_full_unstemmed Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design
title_short Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design
title_sort pre-exascale computing of protein–ligand binding free energies with open source software for drug design
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8924919/
https://www.ncbi.nlm.nih.gov/pubmed/35191702
http://dx.doi.org/10.1021/acs.jcim.1c01445
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