README.md

Oxford Computational Biochemistry Docking Tutorial

Contents

This tutorial teaches the basics of molecular docking.

Here we dock small molecules indinavir and nelfinavir into HIV-1 protease.

Getting started

Please see https://bigginlab.github.io/OxCompBio/docking.html for the tutorial instructions, including installation instructions for the software below.

If you are doing the OxCompBio course, everything has already been setup for you and the required software should work. If you want to do this tutorial on your own, you need to complete the following sections:

Appendix III: Installing the packages locally

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

Requirements

The following software installations are required to do this workshop:

For the molecular docking calculations:

• Autodock Vina

For analysis and visualisation:

• Pymol

Also for analysis and visualisation:

• VMD

Alternative for system preparation (optional):

• AutodockTools

For electrostatics visualization

• APBS