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

被引：3
|
作者：
Bray, Simon [1 ]
Dudgeon, Tim [2 ]
Skyner, Rachael [3 ]
Backofen, Rolf [1 ,4 ]
Gruning, Bjorn [1 ]
von Delft, Frank [3 ,5 ,6 ,7 ]
机构：
[1] Univ Freiburg, Dept Comp Sci, Bioinformat Grp, Freiburg, Germany
[2] Informat Matters, High St, Kidlington, England
[3] Diamond Light Source Ltd, Harwell Sci & Innovat Campus, Didcot, Oxon, England
[4] Univ Freiburg, Signalling Res Ctr BIOSS & CIBSS, Freiburg, Germany
[5] Res Complex Harwell, Harwell Sci & Innovat Campus, Didcot, Oxon, England
[6] Univ Oxford, Struct Genom Consortium, Oxford, England
[7] Univ Johannesburg, Dept Biochem, Johannesburg, South Africa
来源：
JOURNAL OF CHEMINFORMATICS | 2022年 / 14卷 / 01期
关键词：
Fragment screening; Workflows; SARS-CoV-2; Computational chemistry;
D O I：
10.1186/s13321-022-00588-6
中图分类号：
O6 [化学];
学科分类号：
0703 ;
摘要：
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.
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页数：13
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