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FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking

  1. Author:
    Mashiach, E.
    Nussinov, R.
    Wolfson, H. J.

  2. Author Address

    [Mashiach, Efrat; Wolfson, Haim J.] Tel Aviv Univ, Raymond & Beverly Sackler Fac Exact Sci, Blavatnik Sch Comp Sci, IL-69978 Tel Aviv, Israel. [Nussinov, Ruth] NCI Frederick, Basic Sci Program, SAIC Frederick Inc, Ctr Canc Res Nanobiol Program, Frederick, MD 21702 USA. [Nussinov, Ruth] Tel Aviv Univ, Sackler Fac Med, Dept Human Genet & Mol Med, IL-69978 Tel Aviv, Israel.;Wolfson, HJ, Tel Aviv Univ, Raymond & Beverly Sackler Fac Exact Sci, Blavatnik Sch Comp Sci, IL-69978 Tel Aviv, Israel.;wolfson@tau.ac.il
    1. Year: 2010
    2. Date: Jul
  2. Journal: Nucleic Acids Research
    1. 38
    2. Pages: W457-W461
  4. Type of Article: Article
  5. ISSN: 0305-1048
  1. Abstract:

    Protein-protein docking algorithms aim to predict the structure of a complex given the atomic structures of the proteins that assemble it. The docking procedure usually consists of two main steps: docking candidate generation and their refinement. The refinement stage aims to improve the accuracy of the candidate solutions and to identify near-native solutions among them. During protein-protein interaction, both side chains and backbone change their conformation. Refinement methods should model these conformational changes in order to obtain a more accurate model of the complex. Handling protein backbone flexibility is a major challenge for docking methodologies, since backbone flexibility adds a huge number of degrees of freedom to the search space. FiberDock is the first docking refinement web server, which accounts for both backbone and side-chain flexibility. Given a set of up to 100 potential docking candidates, FiberDock models the backbone and side-chain movements that occur during the interaction, refines the structures and scores them according to an energy function. The FiberDock web server is free and available with no login requirement at http://bioinfo3d.cs.tau.ac.il/FiberDock/.

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External Sources

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  2. DOI: 10.1093/nar/gkq373
  3. View record in Web of Science®
  4. WOS: 000284148900074

Library Notes

  1. Fiscal Year: FY2009-2010
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