Classification of Docking by Molecule Type Different types of molecules used in the docking process help to classify molecular docking, a fundamental computational tool used in structural biology and drug development. This classification distinguishes among several docking situations. Each is meant to address specific research hypotheses and objectives. Three varieties of molecular docking models are known to exist: small moleculeprotein ( ), peptide-protein ( ), and protein-protein ( ). Mostly in terms of the scoring systems, they have many parallels. The scoring system determines the strength of the contact between a target and a molecule. The three molecular docking techniques differ mainly in the dimensions of the molecules and the size of the search area.