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dc.contributor.authorStivala, A
dc.contributor.authorWirth, A
dc.contributor.authorStuckey, PJ
dc.date.available2014-05-21T19:46:20Z
dc.date.available2009-05-19
dc.date.available2009-05-19
dc.date.available2009-05-19
dc.date.available2009-05-19
dc.date.available2009-05-19
dc.date.available2009-05-19
dc.date.available2009-05-19
dc.date.issued2009-05-19
dc.identifierpii: 1471-2105-10-153
dc.identifier.citationStivala, 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.
dc.identifier.issn1471-2105
dc.identifier.urihttp://hdl.handle.net/11343/26736
dc.descriptionC1 - Journal Articles Refereed
dc.description.abstractBACKGROUND: 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.
dc.formatapplication/pdf
dc.languageeng
dc.publisherSpringer Science and Business Media LLC
dc.subjectComputer Software not elsewhere classified; Computer Software and Services not elsewhere classified
dc.titleTableau-based protein substructure search using quadratic programming.
dc.typeJournal Article
dc.identifier.doi10.1186/1471-2105-10-153
melbourne.peerreviewPeer Reviewed
melbourne.affiliationThe University of Melbourne
melbourne.affiliation.departmentComputer Science And Software Engineering
melbourne.source.titleBMC Bioinformatics
melbourne.source.volume10
melbourne.source.issue1
melbourne.source.pages153-
dc.research.codefor080399
dc.research.codeseo2008890299
dc.rights.licenseCC BY
melbourne.publicationid131754
melbourne.elementsid314219
melbourne.openaccess.pmchttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705363
melbourne.contributor.authorSTIVALA, ALEXANDER
melbourne.contributor.authorWirth, Anthony
melbourne.contributor.authorStuckey, Peter
dc.identifier.eissn1471-2105
pubs.acceptance.date2009-05-19
melbourne.accessrightsAccess this item via the Open Access location


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