Molecular Docking

An Introduction to Molecular Docking

Welcome back to the Insilco Lab. It is now time to explore the world of molecular docking! 

For Molecular docking, try to picture a lock and a huge box full of thousands of keys that are all different in size and shape. You use a computer to guess which key will fit and open the lock instead of trying each one by hand, which is time-consuming. To save time and money, this is precisely what molecular docking does in the fields of biology and medicine. Scientists use it to understand and predict how different molecules interact with the target of interest (the protein).

You need to be familiar with the following Key Concepts Before We Start

Ligand: The smaller molecule that binds (e.g., a drug candidate, a substrate, an inhibitor). A ligand is usually referred to as a small organic molecule.

Receptor: Is the larger molecule that receives the ligand; it is also known as the target (e.g., a protein, DNA, RNA).

Binding Site: The specific region or "pocket" on the receptor where the ligand binds, because the ligand needs to bind to a specific place on the receptor.

Binding Affinity: Measures how strongly the ligand binds to the receptor, to show the strength of the ligand with the target. It's often predicted as a docking score (measured in kcal/mol). A more negative score indicates stronger binding when analysing the molecular docking results.