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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.

Original publication

DOI

10.1186/s13321-022-00588-6

Type

Journal article

Journal

J Cheminform

Publication Date

12/04/2022

Volume

14

Keywords

Computational chemistry, Fragment screening, SARS-CoV-2, Workflows