Predicting 3D structures of transient protein-protein complexes by homology

The paper reports a homology based approach for predicting the 3D structures of full length hetero protein complexes. We have created a database of templates that includes structures of hetero protein-protein complexes as well as domain-domain structures (), which allowed us to expand the template pool up to 418 two-chain entries (at 40% sequence identity). Two protocols were tested-a protocol based on position specific Blast search (Protocol-I) and a protocol based on structural similarity of monomers (Protocol-II). All possible combinations of two monomers (350,284 pairs) in the ProtCom database were subjected to both protocols to predict if they form complexes. The predictions were benchmarked against the ProtCom database resulting to false-true positives ratios of approximately 5:1 and approximately 7:1 and recovery of 19% and 86%, respectively for protocols I and II. From 350,284 trials Protocol-I made only approximately 500 wrong predictions resulting to 0.5% error. In addition, though it was shown that artificially created domain-domain structures can in principle be good templates for modeling full length protein complexes, more sensitive methods are needed to detect homology relations. The quality of the models was assessed using two different criteria such as interfacial residues and overall RMSD. It was found that there is no correlation between these two measures. In many cases the interface residues were predicted correctly, but the overall RMSD was over 6 A and vice versa.