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Efficient unbound docking of rigid molecules

  1. Author:
    Duhovny, D.
    Nussinov, R.
    Wolfson, H. J.

  2. Author Address

    Duhovny D Tel Aviv Univ, Sch Comp Sci, IL-69978 Tel Aviv, Israel
    1. Year: 2002
  2. Book Title: Algorithms in Bioinformatics, Proceedings
  3. Series Title: Lecture Notes in Computer Science
    1. 2452
    2. Pages: 185-200
  5. Type of Work: Book Chapter
  1. Abstract:

    We present a new algorithm for unbound (real life) docking of molecules, whether protein-protein or protein-drug. The algorithm carries out rigid docking, with surface variability/flexibility implicitly addressed through liberal intermolecular penetration. The high efficiency of the algorithm is the outcome of several factors: (i) focusing initial molecular surface fitting on localized, curvature based surface patches; (ii) use of Geometric Hashing and Pose Clustering for initial transformation detection; (iii) accurate computation of shape complementarity utilizing the Distance Transform; (iv) efficient steric clash detection and geometric fit scoring based on a multi-resolution shape representation; and (v) utilization of biological information by focusing on hot spot rich surface patches. The algorithm has been implemented and applied to a large number of cases.

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