ClusPro: Performance in CAPRI rounds 6-11 and the new server

ClusPro is the first fully automated, web-based program for docking pro tein structures. Users may upload the coordinate files of two protein struc tures through ClusPro's web interface, or enter the PDB codes of the respec tive structures. The server performs rigid body docking, energy screening, and clustering to produce models. The program output is a short list of puta tive complexes ranked according to their clustering properties. ClusPro has been participating in CAPRI since January 2003, submitting predictions within 24 h after a target becomes available. In Rounds 6-11, ClusPro generated acceptable submissions for Targets 22, 25, and 27. In general, ac ceptable models were obtained for the relatively easy targets without substan tial conformational changes upon bind ing. We also describe the new version of ClusPro that incorporates our recently developed docking program PIPER. PIPER is based on the fast Fou rier transform correlation approach, but the method is extended to use pair wise interaction potentials, thereby increasing the number of near-native docked structures.