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ClusPro: Performance in CAPRI rounds 6–11 and the new server
Author(s) -
Comeau Stephen R.,
Kozakov Dima,
Brenke Ryan,
Shen Yang,
Beglov Dmitri,
Vajda Sandor
Publication year - 2007
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21795
Subject(s) - computer science , pairwise comparison , docking (animal) , upload , cluster analysis , web server , protein data bank (rcsb pdb) , macromolecular docking , data mining , theoretical computer science , computational science , operating system , chemistry , artificial intelligence , the internet , stereochemistry , medicine , nursing
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. Proteins 2007. © 2007 Wiley‐Liss, Inc.