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Geometry-based flexible and symmetric protein docking

Authors

  • Dina Schneidman-Duhovny,

    1. School of Computer Science, Beverly and Raymond Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
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    • These authors contributed equally to the work.

  • Yuval Inbar,

    1. School of Computer Science, Beverly and Raymond Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
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    • These authors contributed equally to the work.

  • Ruth Nussinov,

    1. Basic Research Program, SAIC-Frederick, Inc., Laboratory of Experimental and Computational Biology, NCI–Frederick, Frederick, Maryland
    2. Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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    • 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.

  • Haim J. Wolfson

    Corresponding author
    1. School of Computer Science, Beverly and Raymond Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
    • School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
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  • 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.

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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