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

ABSTRACT: 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.

SUBMITTER: Bray S

PROVIDER: S-EPMC9003163 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature

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

Bray Simon S Dudgeon Tim T Skyner Rachael R Backofen Rolf R Grüning Björn B von Delft Frank F

Journal of cheminformatics 20220412 1

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 sys ...[more]

PMID: 35414112

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