This tutorial teaches the basics of molecular docking.
Here we dock small molecules indinavir and nelfinavir into HIV-1 protease.
Please see https://bigginlab.github.io/OxCompBio/docking.html for the tutorial instructions, including installation instructions for the software below.
In order to set everything up before the tutorial, you need to complete the following sections:
- Installing the packages locally
- Obtaining the data files and checking it all works
The actual tutorial starts at section 4.
You can navigate to the other setup instructions through the following:
- Return to the main setup instructions
- Python tutorial setup instructions
- MD tutorial setup instructions
- Homology Modelling setup instructions
The following software installations are required to do this workshop:
For the molecular docking calculations:
For analysis and visualisation:
For system preparation:
- ADFR
- openbabel (http://openbabel.org/wiki/Main_Page)
Alternative for system preparation (optional):
For electrostatics visualization
This tutorial was first created in 2008 as part of the Oxford Wellcome Trust course. It is the product of the work of several authors who have contributed to it over the years. Please see CONTRIBUTORS.md for a full list of acknowledgements. As the tutorial was not originally tracked on github, our apologies if any authors have been missed from this list.
If you happen to contribute to the Docking tutorial, please add yourself to this list!