02. Introduction

2. Introduction

Molecular docking is a computational technique which models the binding interactions between any given ligand and protein. With certain algorithms applied, the resulting array of binding possibilities are ranked in the order of predicted binding affinities. Therefore, whether a molecule can bind to a protein can be estimated with the help of computational power. Such a method is especially useful in structure-based drug design. There are a variety of freely available open-source tools which can enable scientists around the world to have access to these computational techniques and test potential drug molecules via in silico experiments.

This guide is intended to walk you through the processes involved in your molecular docking projects, from target analysis and compound selection to docking experiments and analysis. The manual is a beginner’s guide and requires no prior knowledge of computational techniques, with methods pitched at the Masters or final year undergraduate level.

In this manual, you will learn how to:

1. Use online databases and computational tools to assist drug discovery

2. Use molecular docking techniques via the UCL cluster to perform in silico tests on your compounds