Computational docking analysis This is a snapshot of two adjacent monomers of a pentameric protein called nicotinic Acetyl choline receptor. It is a computational model built on pairwise homology comparison, which was in fact done quite a while ago.

What is shown is part of an N terminal domain connected to its integral membrane protein. In this case, there is a ring-like structure made of five constituent monomer, whilst a drug ( or a small molecule, if you would like) would bind in a pocket formed in between two neighbouring ones.

It is helpful for understanding how the small molecules may bind & pass through the gate-keepers on the membrane, in order for them to be delivered into the cells.

Homology modelling is relatively straightforward, as long as there is an available 3D structure, readily determined and an identified target (for instance via medical genomics, though there can also be other ways) and a good homology comparison between the two, with some luck and skill.