Research Article

Geometry-based flexible and symmetric protein docking†

  1. Dina Schneidman-Duhovny1,‡,
  2. Yuval Inbar1,‡,
  3. Ruth Nussinov2,3,§,
  4. Haim J. Wolfson1,*

Article first published online: 24 JUN 2005

DOI: 10.1002/prot.20562

Issue

Proteins: Structure, Function, and Bioinformatics

Proteins: Structure, Function, and Bioinformatics

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

Volume 60, Issue 2, pages 224–231, 1 August 2005

Additional Information

How to Cite

Schneidman-Duhovny, D., Inbar, Y., Nussinov, R. and Wolfson, H. J. (2005), Geometry-based flexible and symmetric protein docking. Proteins: Structure, Function, and Bioinformatics, 60: 224–231. doi: 10.1002/prot.20562

Author Information

  1. 1

    School of Computer Science, Beverly and Raymond Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel

  2. 2

    Basic Research Program, SAIC-Frederick, Inc., Laboratory of Experimental and Computational Biology, NCI–Frederick, Frederick, Maryland

  3. 3

    Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel

  1. ‡

    These authors contributed equally to the work.

  2. §

    The publisher or recipient acknowledges the right of the U.S. Government to retain a nonexclusive, royalty-free license in and to any copyright covering the article.

*School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel

  1. †

    The content of this publication does not necessarily reflect the view or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organization imply endorsement by the U.S. Government.

Publication History

  1. Issue published online: 24 JUN 2005
  2. Article first published online: 24 JUN 2005
  3. Manuscript Accepted: 7 MAR 2005
  4. Manuscript Received: 16 JAN 2005

Funded by

  • Center of Excellence in Geometric Computing and Its Applications, funded by the Israel Science Foundation (administered by the Israel Academy of Sciences)
  • Hermann Minkowski-Minerva Center for Geometry at Tel Aviv University
  • Federal funds from the National Cancer Institute, National Institutes of Health. Grant Number: NO1-CO-12400

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Keywords:

  • CAPRI;
  • unbound docking;
  • flexible docking;
  • symmetric docking;
  • PatchDock;
  • FlexDock;
  • SymmDock

Abstract

We present a set of geometric docking algorithms for rigid, flexible, and cyclic symmetry docking. The algorithms are highly efficient and have demonstrated very good performance in CAPRI Rounds 3–5. The flexible docking algorithm, FlexDock, is unique in its ability to handle any number of hinges in the flexible molecule, without degradation in run-time performance, as compared to rigid docking. The algorithm for reconstruction of cyclically symmetric complexes successfully assembles multimolecular complexes satisfying Cn symmetry for any n in a matter of minutes on a desktop PC. Most of the algorithms presented here are available at the Tel Aviv University Structural Bioinformatics Web server (http://bioinfo3d.cs.tau.ac.il/). Proteins 2005;60:224–231. © 2005 Wiley-Liss, Inc.

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