Basic Applied Bioinformatics

CHAPTER 35Molecular Docking

CS Mukhopadhyay and HK Manku

School of Animal Biotechnology, GADVASU, Ludhiana

35.1 INTRODUCTION

Docking is an attempt to determine whether two molecules interact with each other, and to find the best match between these two molecules. Biocomputational “docking”, thus, predicts the preferred orientation of one molecule (e.g., protein) bound to another molecule (a ligand) in a lock‐and‐key manner. The particular orientation necessitates overall minimum free energy (ΔG). Docking is necessary because it is a key to rational and sensible drug design. In the process of docking, all intermolecular forces (i.e., H‐bonding, hydrophobicity, dipole–dipole interaction, Van der Waals forces, electrostatic interactions and intra‐molecular forces) and the bond features (i.e., bond length, bond angle, dihedral angle) are taken into account. Docking can be rigid, or there are flexible types. The docking studies are categorized broadly into protein–ligand docking; protein–protein docking; and protein–nucleic acid docking.

35.1.1 Software used for docking

Some of the useful software tools used for docking include Sanjeevani; GOLD; ICM; AUTO DOCK; GLIDE; GRAMM‐X; FlexX; and SwissDock.

35.2 OBJECTIVE

To find the best binding poses of the receptor–ligand complex, based on energy minima of the system.

35.3 PROCEDURE

35.3.1 Target or receptor selection and preparation

The first step of docking is to select a PDB file (protein file for docking with a ligand) and ...