What is Molecular Docking?

The "Lock and Key" Analogy is usually used to describe the molecular docking process.

Molecular docking is a computational method (the use of computers) to predict the preferred orientation of one molecule (ligand) to a second (receptor) when they are bound to each other to form a stable complex.

The "Lock and Key" analogy can be explained as follows:

• The Lock: This is usually a large biological molecule (protein or an enzyme). You need to understand that the proteins are the workhorses of our cells, and their function often depends on their specific 3D shape, which includes pockets or grooves on the surface of the protein. The pocket in the protein is referred to as the "keyhole," which is also known as the binding site.

• The Key: This is typically a small molecule, a natural compound, or a potential therapeutic agent. The key is referred to as the ligand.

The goal of docking is to predict how the "key" (ligand) fits into the "lock" (protein). The docking Simulation tries to find the best-fitting pose (the specific orientation and conformation of the ligand in the protein's binding site). It estimates the strength of the interaction, known as the binding affinity.

Types of Molecular Docking

In computer-aided drug design, molecular docking is divided based on how it handles the molecules' flexibility. The following are the categories of docking simulations.

Rigid docking: The most basic kind is rigid docking. In rigid docking, both the ligand (key) and the protein (lock) are regarded as inflexible, immutable structures.

Flexible ligand docking. The most popular method is flexible ligand docking. During the flexible ligand docking, the ligand is permitted to be flexible while the protein is maintained in its rigid state.

Flexible Docking (or Induced Fit Docking): The most realistic and computationally demanding kind is called flexible docking, also known as induced fit docking. The ligand and the protein are both regarded as flexible.