The area of molecular docking has grown in popularity over the last three decades as structural molecular biology and structure-based drug discovery have become pivotal with time. The tremendous increase in the availability and power of computers, as well as the increased ease of access to small chemical and protein databases, have considerably aided it.
The purpose of automated molecular docking software is to comprehend and predict molecular recognition on both a structural and energetic level, predicting binding affinity. Molecular docking is most commonly done between a small molecule and a macromolecule target. Although ligand–protein docking is commonly used, protein–protein docking is gaining popularity.
Structure–activity studies, lead optimization, virtual screening for potential leads, providing binding hypotheses to aid predictions for mutagenesis studies, assisting x-ray crystallography in the fitting of substrates and inhibitors to electron density, chemical mechanism studies, and combinatorial library design are just a few of the uses and applications of molecular docking in drug discovery.
Virtual screening based on molecular descriptors and physicochemical properties of (in)active ligands is very useful for finding hits and leads through library enrichment for screening, a strategy that is also well-used for reducing and enriching the library of ligands for molecular docking; there are recent reports that ligand shape-matching is as good as, if not better than, docking. When utilised as the final stage in virtual screening, however, molecular docking helps to give three-dimensional (3D) structural theories of how a ligand interacts with its target.