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

Authors

  • Stephen R. Comeau,

    1. Dyax Corp., Cambridge, Massachusetts
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    • Stephen R. Comeau, Dima Kozakov, and Ryan Brenke contributed equally to this work.

  • Dima Kozakov,

    1. BioMolecular Engineering Research Center, Boston University, Boston, Massachusetts
    2. Department of Biomedical Engineering, Boston University, Boston, Massachusetts
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    • Stephen R. Comeau, Dima Kozakov, and Ryan Brenke contributed equally to this work.

  • Ryan Brenke,

    1. BioMolecular Engineering Research Center, Boston University, Boston, Massachusetts
    2. Bioinformatics Graduate Program, Boston University, Boston, Massachusetts
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    • Stephen R. Comeau, Dima Kozakov, and Ryan Brenke contributed equally to this work.

  • Yang Shen,

    1. BioMolecular Engineering Research Center, Boston University, Boston, Massachusetts
    2. Program in Systems Engineering, Boston University, Boston, Massachusetts
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  • Dmitri Beglov,

    1. BioMolecular Engineering Research Center, Boston University, Boston, Massachusetts
    2. Department of Biomedical Engineering, Boston University, Boston, Massachusetts
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  • Sandor Vajda

    Corresponding author
    1. BioMolecular Engineering Research Center, Boston University, Boston, Massachusetts
    2. Department of Biomedical Engineering, Boston University, Boston, Massachusetts
    • Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, MA 02215
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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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