The interaction and docking of two proteins or ligands is the process by which chemical reactions occur on a biological level. One molecule or ligand either inserts itself or closely associates itself with another, and the resulting close association of the two molecules facilitates a particular biological function or cascade of events. For example, the encapsulation of HIV precursor molecules into the binding site of HIV-1 Protease enables the cleavage of the precursor cells into viral components which are then assembled to form the HIV virus.

In order for two molecules to engage and to be able to associate, certain conditions must be met, one of which is that of shape complementarity. It is obvious that if two molecules are to come into close proximity of each other, then the respective sites on the two molecules where the interaction occurs must be receptive to the partner molecule. In the case when a ligand inserts itself wholly into the cleft of another molecule, then the ligand and cleft must be of sufficient size and orientation as to allow the necessary interaction, or else the ligand, the donor molecule, or both of the molecular partners must undergo some sort of change to their three-dimensional structure as to allow the interaction to occur.