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    Tableau-based protein substructure search using quadratic programming.

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    12
    Author
    Stivala, A; Wirth, A; Stuckey, PJ
    Date
    2009-05-19
    Source Title
    BMC Bioinformatics
    Publisher
    Springer Science and Business Media LLC
    University of Melbourne Author/s
    STIVALA, ALEXANDER; Wirth, Anthony; Stuckey, Peter
    Affiliation
    Computer Science And Software Engineering
    Metadata
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    Document Type
    Journal Article
    Citations
    Stivala, A., Wirth, A. & Stuckey, P. J. (2009). Tableau-based protein substructure search using quadratic programming.. BMC Bioinformatics, 10 (1), pp.153-. https://doi.org/10.1186/1471-2105-10-153.
    Access Status
    Access this item via the Open Access location
    URI
    http://hdl.handle.net/11343/26736
    DOI
    10.1186/1471-2105-10-153
    Open Access at PMC
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705363
    Description

    C1 - Journal Articles Refereed

    Abstract
    BACKGROUND: Searching for proteins that contain similar substructures is an important task in structural biology. The exact solution of most formulations of this problem, including a recently published method based on tableaux, is too slow for practical use in scanning a large database. RESULTS: We developed an improved method for detecting substructural similarities in proteins using tableaux. Tableaux are compared efficiently by solving the quadratic program (QP) corresponding to the quadratic integer program (QIP) formulation of the extraction of maximally-similar tableaux. We compare the accuracy of the method in classifying protein folds with some existing techniques. CONCLUSION: We find that including constraints based on the separation of secondary structure elements increases the accuracy of protein structure search using maximally-similar subtableau extraction, to a level where it has comparable or superior accuracy to existing techniques. We demonstrate that our implementation is able to search a structural database in a matter of hours on a standard PC.
    Keywords
    Computer Software not elsewhere classified; Computer Software and Services not elsewhere classified

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