Research Article

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

  1. Stephen R. Comeau1,†,
  2. Dima Kozakov2,3,†,
  3. Ryan Brenke2,4,†,
  4. Yang Shen2,5,
  5. Dmitri Beglov2,3,
  6. Sandor Vajda2,3,*

Article first published online: 17 SEP 2007

DOI: 10.1002/prot.21795

Issue

Proteins: Structure, Function, and Bioinformatics

Proteins: Structure, Function, and Bioinformatics

Special Issue: Third Meeting on the Critical Assessment of PRedicted Interactions

Volume 69, Issue 4, pages 781–785, December 2007

Additional Information

How to Cite

Comeau, S. R., Kozakov, D., Brenke, R., Shen, Y., Beglov, D. and Vajda, S. (2007), ClusPro: Performance in CAPRI rounds 6–11 and the new server. Proteins: Structure, Function, and Bioinformatics, 69: 781–785. doi: 10.1002/prot.21795

Author Information

  1. 1

    Dyax Corp., Cambridge, Massachusetts

  2. 2

    BioMolecular Engineering Research Center, Boston University, Boston, Massachusetts

  3. 3

    Department of Biomedical Engineering, Boston University, Boston, Massachusetts

  4. 4

    Bioinformatics Graduate Program, Boston University, Boston, Massachusetts

  5. 5

    Program in Systems Engineering, Boston University, Boston, Massachusetts

  1. †

    Stephen R. Comeau, Dima Kozakov, and Ryan Brenke contributed equally to this work.

*Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, MA 02215

Publication History

  1. Issue published online: 31 OCT 2007
  2. Article first published online: 17 SEP 2007
  3. Manuscript Accepted: 17 JUL 2007
  4. Manuscript Revised: 13 JUL 2007
  5. Manuscript Received: 7 JUN 2007

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Keywords:

  • protein docking;
  • web-based computing;
  • docking server;
  • fast fourier transform correlation method;
  • discrimination by clustering

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. Proteins 2007. © 2007 Wiley-Liss, Inc.

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