Research Article

Docking with PIPER and refinement with SDU in rounds 6–11 of CAPRI

  1. Yang Shen1,2,†,
  2. Ryan Brenke1,3,†,
  3. Dima Kozakov1,4,†,
  4. Stephen R. Comeau5,†,
  5. Dmitri Beglov1,4,
  6. Sandor Vajda1,4,*

Article first published online: 12 SEP 2007

DOI: 10.1002/prot.21754

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 734–742, December 2007

Additional Information

How to Cite

Shen, Y., Brenke, R., Kozakov, D., Comeau, S. R., Beglov, D. and Vajda, S. (2007), Docking with PIPER and refinement with SDU in rounds 6–11 of CAPRI. Proteins: Structure, Function, and Bioinformatics, 69: 734–742. doi: 10.1002/prot.21754

Author Information

  1. 1

    BioMolecular Engineering Research Center, Boston University, Boston, Massachusetts

  2. 2

    Program in Systems Engineering, Boston University, Boston, Massachusetts

  3. 3

    Program in Bioinformatics, Boston University, Boston, Massachusetts

  4. 4

    Department of Biomedical Engineering, Boston University, Boston, Massachusetts

  5. 5

    Dyax Corp., Boston, Massachusetts

  1. †

    Yang Shen, Ryan Brenke, Dima Kozakov, and Stephen R. Comeau 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: 12 SEP 2007
  3. Manuscript Accepted: 18 JUL 2007
  4. Manuscript Revised: 13 JUL 2007
  5. Manuscript Received: 5 JUN 2007

Funded by

  • National Institute of Health. Grant Numbers: GM061867, GM079396
  • National Science Foundation. Grant Number: MRI DBI-0116574

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Keywords:

  • fast Fourier transform;
  • clustering;
  • energy funnel;
  • protein docking by PIPER;
  • refinement by SDU;
  • global optimization;
  • semidefinite programming;
  • DARS pairwise potential

Abstract

Our approach to protein–protein docking includes three main steps. First we run PIPER, a new rigid body docking program. PIPER is based on the Fast Fourier Transform (FFT) correlation approach that has been extended to use pairwise interactions potentials, thereby substantially increasing the number of near-native structures generated. The interaction potential is also new, based on the DARS (Decoys As the Reference State) principle. In the second step, the 1000 best energy conformations are clustered, and the 30 largest clusters are retained for refinement. Third, the conformations are refined by a new medium-range optimization method SDU (Semi-Definite programming based Underestimation). SDU has been developed to locate global minima within regions of the conformational space in which the energy function is funnel-like. The method constructs a convex quadratic underestimator function based on a set of local energy minima, and uses this function to guide future sampling. The combined method performed reliably without the direct use of biological information in most CAPRI problems that did not require homology modeling, providing acceptable predictions for targets 21, and medium quality predictions for targets 25 and 26. Proteins 2007. © 2007 Wiley-Liss, Inc.

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