Molecular docking is a method used to predict the binding mode of the molecular complex formed by two binding partners.
In small molecule docking, the aim is to predict how a small molecule, such as a drug, binds to a target biomacromolecule. There are a large number of docking methods that use different search algorithms to sample the conformational space available to the molecule within the target's binding site. Each docking method also requires a scoring function, which is able to give a fast estimation of the binding free energy of a given binding orientation, or pose. The scoring function may be used during the conformational search, and is also used to rank the different poses of a given small molecule, and to compare the most favorable poses of different molecules.
Autodock, GOLD and Glide are some of the most commonly used protein-ligand docking software suites in the research community.