In this tutorial, we introduce the fast way for drug virtual screening of SARS-CoV-2 Mpro based on the known database such as ZINC database. The premise for this tutorial is that you can deal with protein structure for Autodock Vina. If you are not familiar with it, you can learn from the previous tutorial https://github.com/MolAICal/documents/tree/master/tutorials/002-AIVS. Here, MolAICal (https://doi.org/10.1093/bib/bbaa161) is employed for this tutorial.
2. Materials
2.1. Software requirement
1) MolAICal: https://molaical.github.io
2.2. Example files
1) All the necessary tutorial files are downloaded from:
https://github.com/MolAICal/tutorials/tree/master/003-VS
2) The file named “ligandSet.mol2” which contains 16 ligands obtained from ZINC database is chosen for demo. You can select your ligand database.
3) The protein file named “pro.pdbqt” that is PDBQT format structure of SARS-CoV-2 Mpro is used for molecular docking.
For more detailed procedures, please go to https://molaical.github.io, and click the section named "Tutorials" in the left part of webpage. Once "Tutorials" open, you can freely find pdf file about this tutorial (see Figure 1):
You can repeat this tutorial according to the content of pdf file.
