Show simple item record

dc.contributor.authorStivala, A
dc.contributor.authorWirth, A
dc.contributor.authorStuckey, PJ
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-.
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.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
melbourne.peerreviewPeer Reviewed
melbourne.affiliationThe University of Melbourne
melbourne.affiliation.departmentComputer Science And Software Engineering
melbourne.source.titleBMC Bioinformatics
dc.rights.licenseCC BY
melbourne.contributor.authorSTIVALA, ALEXANDER
melbourne.contributor.authorWirth, Anthony
melbourne.contributor.authorStuckey, Peter
melbourne.accessrightsAccess this item via the Open Access location

Files in this item


There are no files associated with this item.

This item appears in the following Collection(s)

Show simple item record