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Efficient Unbound Docking of Rigid Molecules

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Algorithms in Bioinformatics (WABI 2002)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2452))

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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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Author information

Authors and Affiliations

  1. School of Computer Science, Tel Aviv University, 69978, Tel Aviv, Israel

    Dina Duhovny & Haim J. Wolfson

  2. Sackler Inst. of Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Israel

    Ruth Nussinov

  3. IRSP - SAIC, Lab. of Experimental and Computational Biology, NCI - FCRDC, Bldg 469, Rm 151, 21702, Frederick, MD, USA

    Ruth Nussinov

Authors
  1. Dina Duhovny
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  2. Ruth Nussinov
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  3. Haim J. Wolfson
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Editor information

Editors and Affiliations

  1. IMIM-UPF-CRG, Dr. Aiguader 80, 08003, Barcelona, Spain

    Roderic Guigó

  2. Department of Computer Science, University of California, 95616, Davis, CA, USA

    Dan Gusfield

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© 2002 Springer-Verlag Berlin Heidelberg

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Duhovny, D., Nussinov, R., Wolfson, H.J. (2002). Efficient Unbound Docking of Rigid Molecules. In: Guigó, R., Gusfield, D. (eds) Algorithms in Bioinformatics. WABI 2002. Lecture Notes in Computer Science, vol 2452. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45784-4_14

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  • DOI: https://doi.org/10.1007/3-540-45784-4_14

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-44211-0

  • Online ISBN: 978-3-540-45784-8

  • eBook Packages: Springer Book Archive

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