A new drug development may cost about 2.6 billion USD. However, about 90% of drugs are failure in the process of clinical trial and approval for marketing even though a lot of capital is used to drug development1. In this tutorial, the standard protocol of MolAICal (https://doi.org/10.1093/bib/bbaa161) is introduced for the drug design of SARS-CoV-2 Mpro by artificial intelligence and molecular docking method. It will help the pharmacologist, chemists and other scientists design rational drugs according to the three-dimensional active pocket of proteins.
2. Materials
2.1. Software requirement
1) MolAICal (win64 or linux64): https://molaical.github.io
2) UCSF Chimera: https://www.cgl.ucsf.edu/chimera/
3) MGLTools: https://ccsb.scripps.edu/mgltools/downloads/
4) Python: https://www.python.org/
5) Pymol: http://www.lfd.uci.edu/~gohlke/pythonlibs
It is easily to install the first four software. They can be easily installed by following step tips. For pymol install, it needs modules numpy, pmw, pymol_launcher and pymol. The numpy, pmw, pymol_launcher and pymol should choose the same version and correspond to your installed version of Python in your operating system. They can be downloaded from the below website:
https://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy
https://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol-open-source
Then install Pymol by following command:
#> pip install --no-index --find-links="%CD%" pymol_launcher
The Pymol named “pymol.exe” will be installed in the directory “Scripts” in your installed directory of Python. You can make a shortcut on your desktop of operating system.
Make sure all software is installed rightly.
2.2. Example files
All the necessary tutorial files are downloaded from:
https://github.com/MolAICal/tutorials/tree/master/002-AIVS
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.
