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

Simon Bray; Tim Dudgeon; Rachael Skyner; Rolf Backofen; Björn Grüning; Frank von Delft

doi:10.1186/s13321-022-00588-6

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

J Cheminform. 2022 Apr 12;14(1):22. doi: 10.1186/s13321-022-00588-6.

Authors

Simon Bray¹, Tim Dudgeon², Rachael Skyner^{3

4}, Rolf Backofen^{5

6}, Björn Grüning⁵, Frank von Delft^{3

4

7

8}

Affiliations

¹ Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg im Breisgau, Germany. sbray@informatik.uni-freiburg.de.
² Informatics Matters, Yew Tree Farm, High Street, Charlton on Otmoor, Kidlington, UK.
³ Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, UK.
⁴ Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, UK.
⁵ Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg im Breisgau, Germany.
⁶ Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg im Breisgau, Germany.
⁷ Structural Genomics Consortium, University of Oxford, Oxford, UK.
⁸ Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa.

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.

Keywords: Computational chemistry; Fragment screening; SARS-CoV-2; Workflows.

Abstract

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