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Prediction of the unknown: Inspiring experience with the CAPRI experiment

Authors

  • Efrat Ben-Zeev,

    1. Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
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    • E.B.Z., A.B., A.H., and B.S. contributed equally and are listed in alphabetical order.

  • Alexander Berchanski,

    1. Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
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    • E.B.Z., A.B., A.H., and B.S. contributed equally and are listed in alphabetical order.

  • Alexander Heifetz,

    1. Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
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    • E.B.Z., A.B., A.H., and B.S. contributed equally and are listed in alphabetical order.

  • Boaz Shapira,

    1. Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
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    • E.B.Z., A.B., A.H., and B.S. contributed equally and are listed in alphabetical order.

  • Miriam Eisenstein

    Corresponding author
    1. Chemical Services, The Weizmann Institute of Science, Rehovot, Israel
    • Department of Chemical Services, The Weizmann Institute of Science, Rehovot 76100, Israel
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Abstract

We submitted predictions for all seven targets in the CAPRI experiment. For four targets, our submitted models included acceptable, medium accuracy predictions of the structures of the complexes, and for a fifth target we identified the location of the binding site of one of the molecules. We used a weighted-geometric docking algorithm in which contacts involving specified parts of the surfaces of either one or both molecules were up-weighted or down-weighted. The weights were based on available structural and biochemical data or on sequence analyses. The weighted-geometric docking proved very useful for five targets, improving the complementarity scores and the ranks of the nearly correct solutions, as well as their statistical significance. In addition, the weighted-geometric docking promoted formation of clusters of similar solutions, which include more accurate predictions. Proteins 2003;52:41–46. © 2003 Wiley-Liss, Inc.

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