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Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function

Authors

  • Chi Zhang,

    1. Howard Hughes Medical Institute Center for Single Molecule Biophysics, Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York
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    • These two authors contributed equally to this work.

  • Song Liu,

    1. Howard Hughes Medical Institute Center for Single Molecule Biophysics, Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York
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    • These two authors contributed equally to this work.

  • Yaoqi Zhou

    Corresponding author
    1. Howard Hughes Medical Institute Center for Single Molecule Biophysics, Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York
    2. Department of Macromolecular Science, Key Laboratory of Molecular Engineering of Polymers, Fudan University, China
    • Howard Hughes Medical Institute Center for Single Molecule Biophysics and Department of Physiology and Biophysics, State University of New York at Buffalo, 124 Sherman Hall, Buffalo, NY 14214
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Abstract

We entered the CAPRI experiment during the middle of Round 4 and have submitted predictions for all 6 targets released since then. We used the following procedures for docking prediction: (1) the identification of possible binding region(s) of a target based on known biological information, (2) rigid-body sampling around the binding region(s) by using the docking program ZDOCK, (3) ranking of the sampled complex conformations by employing the DFIRE-based statistical energy function, (4) clustering based on pairwise root-mean-square distance and the DFIRE energy, and (5) manual inspection and relaxation of the side-chain conformations of the top-ranked structures by geometric constraint. Reasonable predictions were made for 4 of the 6 targets. The best fraction of native contacts within the top 10 models are 89.1% for Target 12, 54.3% for Target 13, 29.3% for Target 14, and 94.1% for Target 18. The origin of successes and failures is discussed. Proteins 2005;60:314–318. © 2005 Wiley-Liss, Inc.

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