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

01 December 2021, Version 1
Working Paper
This content is a preprint and has not undergone peer review at the time of posting.

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 40000 compounds against the SARS-CoV-2 main protease, a system which has been the subject of intense study in the last year.

Keywords

fragment screening
workflows
SARS-CoV-2
computational chemistry

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Version History

Dec 01, 2021 Version 1

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The content is available under CC BY NC ND 4.0 [opens in a new tab]

DOI

10.26434/chemrxiv-2021-zr4xn
D O I: 10.26434/chemrxiv-2021-zr4xn [opens in a new tab]

Author’s competing interest statement

The author(s) have declared they have no conflict of interest with regard to this content

Ethics

The author(s) have declared ethics committee/IRB approval is not relevant to this content

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