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Efficient Unbound Docking of Rigid Molecules

  • Dina Duhovny
  • Ruth Nussinov
  • Haim J. Wolfson
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2452)

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.

Keywords

Surface Point Molecular Surface Protein Docking Steric Clash Docking Algorithm 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2002

Authors and Affiliations

  • Dina Duhovny
    • 1
  • Ruth Nussinov
    • 2
    • 3
  • Haim J. Wolfson
    • 1
  1. 1.School of Computer ScienceTel Aviv UniversityTel AvivIsrael
  2. 2.Sackler Inst. of Molecular Medicine, Sackler Faculty of MedicineTel Aviv UniversityIsrael
  3. 3.IRSP - SAICLab. of Experimental and Computational Biology, NCI - FCRDCFrederickUSA

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