POL Scientific / JBM / Volume 8 / Issue 4 / DOI: 10.14440/jbm.2021.351
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PROTOCOLS

Virtual screening on the web for drug repurposing: a primer

Yu Wai Chen1 Chin-Pang Bennu Yiu2 Kwok-Yin Wong1
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1 Hong Kong Polytechnic University, Hong Kong Polytechnic University
2 Independent Researcher, Independent Researcher
Published: 26 May 2021
(This article belongs to the Special Issue Methods to Facilitate SARS-CoV-2 and COVID-19 Research)
© 2021 by the author. Licensee POL Scientific, USA. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution 4.0 International License ( https://creativecommons.org/licenses/by/4.0/ )
Abstract

We describe a procedure of performing in silico (virtual) screening using a web-based service, the MTiOpenScreen, which
is freely accessible to non-commercial users. We shall use the SARS-CoV-2 main protease as an example. Starting from a structure downloaded from the Protein Data Bank, we discuss how to prepare the coordinates file, taking into account the known biochemical background information of the target protein. The reader will find that this preparation step takes up most of the effort before the target is ready for screening. The steps for uploading the target structure and defining the search volume by critical residues, and the main parameters to use, are outlined. When this protocol is followed, the user will expect to obtain a ranked list of small approved drug compounds docked into the target structure. The results can be readily examined graphically on the web site or downloaded for studying in a local molecular graphics program such as PyMOL.

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Journal of Biological Methods, Electronic ISSN: 2326-9901 Print ISSN: TBA, Published by POL Scientific