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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Detalles Bibliográficos
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
Descripción
Sumario: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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