Abstract

Cheminformatics is the use of computational techniques and information about molecules to solve problems in chemistry. This involves a number of steps: retrieving data on chemical compounds, sorting data for properties which are of interest, and extracting new information. This tutorial will provide a brief overview of all of these, centered around protein-ligand docking, a molecular modelling technique. The purpose of protein-ligand docking is to find the optimal binding between a small molecule (ligand) and a protein. It is generally applied to the drug discovery and development process with the aim of finding a potential drug candidate. First, a target protein is identified. This protein is usually linked to a disease and is known to bind small molecules. Second, a 'library' of possible ligands is assembled. Ligands are small molecules that bind to a protein and may interfere with protein function. Each of the compounds in the library is then 'docked' into the protein to find the optimal binding position and energy.

About This Material

This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.

Questions this will address

• What is cheminformatics?
• What is protein-ligand docking?
• How can I perform a simple docking workflow in Galaxy?

Learning Objectives

• Create a small compound library using the ChEMBL database
• Dock a variety of ligands to the active site of the Hsp90 protein