A novel method for scoring of docked protein complexes using predicted protein-protein binding sites

Docking algorithms produce many possible structures of a protein-protein complex. In most cases some of them resemble the correct structure within an r.m.s.d. of <3 A. A major challenge in the field of docking is to extract the correct structure out of this pool, the so-called 'scoring'. Here, we introduce a new scoring function, which discriminates between the many wrong and few true conformations. The scoring function is based on measuring the tightness of fit of the two docked proteins at a predicted binding interface. The location of the binding interface is identified using the recently developed computer algorithm ProMate. The new scoring function does not rely on energy considerations. It is therefore tolerant to low-resolution descriptions of the interface. A linear relation between the score and the r.m.s.d. relative to the 'true structure' is found in most of the cases evaluated. The function was tested on the docking results of 21 complexes in their unbound form. It was found to be successful in 77% of the examined cases, defining success as scoring a 'true' result with a p value of better than 0.1.