Virtual screening on the web for drug repurposing: a primer

Authors

  • Yu Wai Chen Hong Kong Polytechnic University
  • Chin-Pang Bennu Yiu Independent Researcher
  • Kwok-Yin Wong Hong Kong Polytechnic University

DOI:

https://doi.org/10.14440/jbm.2021.351

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.

Author Biography

Yu Wai Chen, Hong Kong Polytechnic University

Department of Applied Biology and Chemical Technology

Senior Research Fellow

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Published

2021-05-26

How to Cite

1.
Chen YW, Yiu C-PB, Wong K-Y. Virtual screening on the web for drug repurposing: a primer. J Biol Methods [Internet]. 2021May26 [cited 2021Oct.21];8(COVID 19 Special Issue):e148. Available from: https://jbmethods.org/jbm/article/view/351