Tableau-based protein substructure search using quadratic programming.
AuthorStivala, A; Wirth, A; Stuckey, PJ
Source TitleBMC Bioinformatics
PublisherSpringer Science and Business Media LLC
AffiliationComputer Science And Software Engineering
Document TypeJournal Article
CitationsStivala, 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 StatusAccess this item via the Open Access location
Open Access at PMChttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705363
C1 - Journal Articles Refereed
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.
KeywordsComputer Software not elsewhere classified; Computer Software and Services not elsewhere classified
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