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Rapid Protein Side-Chain Packing via Tree Decomposition

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Research in Computational Molecular Biology (RECOMB 2005)

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

Abstract

This paper proposes a novel tree decomposition based side-chain assignment algorithm, which can obtain the globally optimal solution of the side-chain packing problem very efficiently. Theoretically, the computational complexity of this algorithm is O((N + M)n \(_{rot}^{tw + 1}\)) where N is the number of residues in the protein, M the number of interacting residue pairs, n rot the average number of rotamers for each residue and \(O((N + M)n^{tw+1}_{rot})\) the tree width of the residue interaction graph. Based on this algorithm, we have developed a side-chain prediction program SCATD (Side Chain Assignment via Tree Decomposition). Experimental results show that after the Goldstein DEE is conducted, n rot is around 3.5, tw is only 3 or 4 for most of the test proteins in the SCWRL benchmark and less than 10 for all the test proteins. SCATD runs up to 90 times faster than SCWRL 3.0 on some large proteins in the SCWRL benchmark and achieves an average of five times faster speed on all the test proteins. If only the post-DEE stage is taken into consideration, then our tree-decomposition based energy minimization algorithm is more than 200 times faster than that in SCWRL 3.0 on some large proteins. SCATD is freely available for academic research upon request.

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Author information

Authors and Affiliations

  1. School of Computer Science, University of Waterloo, Waterloo, Ontario, N2L 3G1

    Jinbo Xu

  2. Department of Mathematics, MIT, Cambridge, MA, 02139, Canada

    Jinbo Xu

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  1. Jinbo Xu
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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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Xu, J. (2005). Rapid Protein Side-Chain Packing via Tree Decomposition. 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_32

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  • DOI: https://doi.org/10.1007/11415770_32

  • 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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