Bioinformatics Tools Training Program

PyRx is an open source software to perform virtual screening. It is a combination of several softwares such as AutoDock Vina, AutoDock 4.2, Mayavi, Open Babel, etc. PyRx uses Vina and
AutoDock 4.2 as docking softwares. PyRx is a Virtual Screening software for Computational Drug
Discovery that can be used to screen libraries of compounds against potential drug targets. PyRx
enables Medicinal Chemists to run Virtual Screening from any platform and helps users in every
step of this process – from data preparation to job submission and analysis of the results. While it is
true that there is no magic button in the drug discovery process, PyRx includes docking wizard with
an easy-to-use user interface which makes it a valuable tool for Computer-Aided Drug Design.
PyRx also includes chemical spreadsheet-like functionality and powerful visualization engine that
are essential for structure-based drug design.

1. Downloading the PyRx – http://pyrx.sourceforge.net/downloads
2. Loading molecules into PyRx workspace
3.Use upper left button as shown in the figure to load your proteinand ligand (s)into PyRx
workspace.
4.After successfully loading molecules in to the workspace, convert them into AutoDock input files
(pdbqt files)as shown below.
5.Right click on ligand(s) > AutoDock> Make ligand
6.Right click on protein> AutoDock> Make Macromolecule
7. After converting pdb files into AutoDock input files (or .pdbqt files), you will see them under
AutoDocktab as shown below (if you don’t see any files, right click and refresh under AutoDock
tab)
8. Now the protein and ligand(s) files are ready for docking.
9.Click on Start Here button under Vina Wizard.
10. Select Local button under Vina executioinMode
11. Click Start Button.
12. Select protein and ligand(s) by simply clicking on them. You will see a window like below (In
the picture below we selected two ligand and one macromolecule).
13. Click Forward to Run Vina
14. In this step you will see a grid box (white box with spherical handles)in the 3D scene as shown
below. This grid box allows you to select search space (Part of the protein, where we are going to
perform docking,typically the binding site) in the protein.
15.Results can be exported to other software programs like UCSF Chimera or Pymolfor analysis.