Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease

We present several workflows for protein-ligand docking and free energy calculation for use in the workflow management system Galaxy. The workflows are composed of several widely used open-source tools, including rDock and GROMACS, and can be executed on public infrastructure using either Galaxy’s g...

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Autores principales: Bray, Simon, Dudgeon, Tim, Skyner, Rachael, Backofen, Rolf, Grüning, Björn, von Delft, Frank
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer International Publishing 2022
Materias:
Research Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9003163/
https://www.ncbi.nlm.nih.gov/pubmed/35414112
http://dx.doi.org/10.1186/s13321-022-00588-6
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author Bray, Simon
Dudgeon, Tim
Skyner, Rachael
Backofen, Rolf
Grüning, Björn
von Delft, Frank
author_facet Bray, Simon
Dudgeon, Tim
Skyner, Rachael
Backofen, Rolf
Grüning, Björn
von Delft, Frank
author_sort Bray, Simon
collection PubMed
description We present several workflows for protein-ligand docking and free energy calculation for use in the workflow management system Galaxy. The workflows are composed of several widely used open-source tools, including rDock and GROMACS, and can be executed on public infrastructure using either Galaxy’s graphical interface or the command line. We demonstrate the utility of the workflows by running a high-throughput virtual screening of around 50000 compounds against the SARS-CoV-2 main protease, a system which has been the subject of intense study in the last year. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13321-022-00588-6.
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spelling pubmed-90031632022-04-12 Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease Bray, Simon Dudgeon, Tim Skyner, Rachael Backofen, Rolf Grüning, Björn von Delft, Frank J Cheminform Research Article We present several workflows for protein-ligand docking and free energy calculation for use in the workflow management system Galaxy. The workflows are composed of several widely used open-source tools, including rDock and GROMACS, and can be executed on public infrastructure using either Galaxy’s graphical interface or the command line. We demonstrate the utility of the workflows by running a high-throughput virtual screening of around 50000 compounds against the SARS-CoV-2 main protease, a system which has been the subject of intense study in the last year. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13321-022-00588-6. Springer International Publishing 2022-04-12 /pmc/articles/PMC9003163/ /pubmed/35414112 http://dx.doi.org/10.1186/s13321-022-00588-6 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research Article
Bray, Simon
Dudgeon, Tim
Skyner, Rachael
Backofen, Rolf
Grüning, Björn
von Delft, Frank
Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease
title Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease
title_full Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease
title_fullStr Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease
title_full_unstemmed Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease
title_short Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease
title_sort galaxy workflows for fragment-based virtual screening: a case study on the sars-cov-2 main protease
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9003163/
https://www.ncbi.nlm.nih.gov/pubmed/35414112
http://dx.doi.org/10.1186/s13321-022-00588-6
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