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Recognition of Binding Patterns Common to a Set of Protein Structures

  • Conference paper
Research in Computational Molecular Biology (RECOMB 2005)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 3500))

Abstract

We present a novel computational method, MultiBind, for recognition of binding patterns common to a set of protein structures. It is the first method which performs a multiple alignment between protein binding sites in the absence of overall sequence, fold or binding partner similarity. MultiBind recognizes common spatial arrangements of physico-chemical properties in the binding sites. These should be important for recognition of function, prediction of binding and drug design. We discuss the theoretical aspects of the computational problem of multiple structure alignment. This problem involves solving a 3D k-partite matching problem, which we show to be NP-Hard. The MultiBind method, applies an efficient Geometric Hashing technique to detect a potential set of multiple alignments of the given binding sites. To overcome the exponential number of possible multiple combinations it applies a very efficient filtering procedure which is heavily based on the selected scoring function. Our method guarantees detection of an approximate solution in terms of pattern proximity as well as cardinality of multiple alignment. We show applications of MultiBind to several biological targets. The method recognizes patterns which are responsible for binding small molecules such as estradiol, ATP/ANP and transition state analogues. The presented computational results agree with the available biological ones.

Availability: http://bioinfo3d.cs.tau.ac.il/MultiBind/.

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Author information

Authors and Affiliations

  1. School of Computer Science, Raymond and Beverly Sackler, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 69978, Israel

    Maxim Shatsky, Alexandra Shulman-Peleg & Haim J. Wolfson

  2. Sackler Inst. of Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel

    Ruth Nussinov

  3. Basic Research Program, SAIC-Frederick, Inc, Lab. of Experimental and Computational Biology, Bldg. 469, Rm. 151, Frederick, MD, 21702, USA

    Ruth Nussinov

Authors
  1. Maxim Shatsky
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  2. Alexandra Shulman-Peleg
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  3. Ruth Nussinov
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  4. Haim J. Wolfson
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Editor information

Editors and Affiliations

  1. Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, 108-8639, Minato-ku, Tokyo, Japan

    Satoru Miyano

  2. Broad Institute of MIT and Harvard, 320 Charles Street, 02141-2023, Cambridge, MA, USA

    Jill Mesirov

  3. Computational Genomics Laboratory, Department of Bioengineering, Boston University, 44 Cummington St., 02215, Boston, MA, USA

    Simon Kasif

  4. Center for Molecular Biology and Computer Sciecne Department, Brown University, 115 Waterman St., 02912, Providence, RI, USA

    Sorin Istrail

  5. University of California, San Diego, USA

    Pavel A. Pevzner

  6. Department of Molecular and Computational Biology, University of Southern California, 1050 Childs Way, 90089-2910, Los Angeles, CA, USA

    Michael Waterman

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© 2005 Springer-Verlag Berlin Heidelberg

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Shatsky, M., Shulman-Peleg, A., Nussinov, R., Wolfson, H.J. (2005). Recognition of Binding Patterns Common to a Set of Protein Structures. In: Miyano, S., Mesirov, J., Kasif, S., Istrail, S., Pevzner, P.A., Waterman, M. (eds) Research in Computational Molecular Biology. RECOMB 2005. Lecture Notes in Computer Science(), vol 3500. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11415770_33

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  • DOI: https://doi.org/10.1007/11415770_33

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-25866-7

  • Online ISBN: 978-3-540-31950-4

  • eBook Packages: Computer ScienceComputer Science (R0)

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