Successful discrimination of protein interactions

We present results from the prediction of protein complexes associated with the first Critical Assessment of PRediction of Interactions (CAPRI) experiment. Our algorithm, SmoothDock, comprises four steps: (1) we perform rigid body docking using the program DOT, keeping the top 20,000 structures as ranked by surface complementarity; (2) we rerank these structures according to a free energy estimate that includes both desolvation and electrostatics and retain the top 2000 complexes; (3) we cluster the filtered complexes using a pairwise root-mean-square deviation (RMSD) criterion; (4) the 25 largest clusters are subject to a smooth docking discrimination algorithm where van der Waals forces are taken into account. We predicted targets 1, 6, and 7 with RMSDs of 9.5, 2.4, and 2.6 A, respectively. More importantly, from the perspective of biological applications, our approach consistently ranked the correct model first (i.e., with highest confidence). For target 5 we identified the binding region but not the correct orientation. Although we were able to find reasonable clusters for all targets, low-affinity complexes (K(d) < nM) were harder to discriminate. For four of seven targets, the top models predicted by our automated procedure were among the best communitywide predictions.