Protein surface conservation in binding sites.

An algorithm is described which uses the conservation of the 3D structure of protein surfaces, as opposed to their sequences, to detect protein-protein binding sites. The protein in which protein-protein binding sites are sought is compared with structures of multiple structurally related proteins and the surface that is conserved at least once is considered to be a part of the binding site. The binding site predictions obtained in this way for a set of protein-protein complexes correspond well with the actual protein-protein binding sites. A comparison of this method with an algorithm using the support vector machine approach for predicting protein-protein binding sites shows structural conservation to be an important characteristic that distinguishes binding sites from the remainder of protein surfaces.