Computational docking

Computational docking is a technique with which one predicts the 3D structure of the complex between two or more molecules. Typically, its applications are confined to protein-protein complexes and to associations between proteins and small molecules. The 3D structure of the individual partners must be known and it is possible to consider computational docking as an extension of the modelling techniques, used to predict 3D structure of proteins. Computationally it is possible to determine the 3D structure of complexes that cannot be obtained through experimental techniques like crystallography or NMR spectroscopy.

A number of inter-molecular interactions are in fact transient, from a kinetics point of view, or weak, from a thermodynamics point of view. Consequently they cannot be studied experimentally, since the average concentration of the complex is too low. Computational docking is therefore the only possibility to determine the 3D features of these types of inter-molecular associations.