title: ClusPro: performance in CAPRI rounds 6-11 and the new server.
abstract: ClusPro is the first fully automated, web-based program for docking protein structures. Users may upload the coordinate files of two protein structures through ClusPro's web interface, or enter the PDB codes of the respective structures. The server performs rigid body docking, energy screening, and clustering to produce models. The program output is a short list of putative 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, acceptable models were obtained for the relatively easy targets without substantial conformational changes upon binding. We also describe the new version of ClusPro that incorporates our recently developed docking program PIPER. PIPER is based on the fast Fourier transform correlation approach, but the method is extended to use pairwise interaction potentials, thereby increasing the number of near-native docked structures.
authors: Dyax Corp., Cambridge, Massachusetts, USA.
authors: Stephen R
authors: SR
authors: Comeau
authors: Dima
authors: D
authors: Kozakov
authors: Ryan
authors: R
authors: Brenke
authors: Yang
authors: Y
authors: Shen
authors: Dmitri
authors: D
authors: Beglov
authors: Sandor
authors: S
authors: Vajda
mesh_terms: D000465:Algorithms; D001331:Automation; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D030562:Databases, Protein; D019281:Dimerization; D004867:Equipment Design; D004926:Escherichia coli / Q000378:metabolism; D023281:Genomics; D020407:Internet; D008968:Molecular Conformation; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins