Protein-protein docking in CAPRI using ATTRACT to account for global and local flexibility

A reduced protein model com bined with a systematic dock ing approach has been employed to predict protein- protein complex structures in CAPRI rounds 6-11. The docking approach termed ATTRACT is based on energy minimization in translational and rotational degrees of free dom of one protein with respect to the second protein starting from many thousand initial protein partner place ments. It also allows for ap proximate inclusion of global flexibility of protein partners during systematic docking by conformational relaxation of the partner proteins in precal culated soft collective back bone degrees of freedom. We have submitted models for six targets, achieved acceptable docking solutions for two tar gets, and predicted >20% cor rect contacts for five targets. Possible improvements of the docking approach in particu lar at the scoring and refine ment steps are discussed.