Evolutionary Docking of Proteins

The coupled evolution of pairs of positions is the cornerstone in the prediction of RNA secondary structure and thus the position of RNA genes in DNA sequences. There have been similar attempts to use such dependencies to predict which protein residues were in physical proximity. However, these attempts have clearly been much less successful in protein than in RNA. Nevertheless, success of this could be very useful and we here propose a new version of this problem that differs from old versions in two aspects: Firstly, the application is the interaction between known structures determined by structural genomics projects. Secondly, it is coupled to another predictive method namely docking that by geometric or physical characterization tries to find complementary regions in structures that are likely to interact. This last facet allows a ranking of the search space (all possible pairs of residues) by using the structural knowledge to immediately discard sets of interactions that are physically impossible. If successful the method will predict positions that interact among pairs of structures.