Smolign: a spatial motifs-based protein multiple structural alignment method

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dc.citation.epage261en_US
dc.citation.issueNumber1en_US
dc.citation.spage249en_US
dc.citation.volumeNumber9en_US
dc.contributor.authorSun, H.en_US
dc.contributor.authorSacan, A.en_US
dc.contributor.authorFerhatosmanoglu, H.en_US
dc.contributor.authorWang Y.en_US
dc.date.accessioned2019-02-20T14:11:35Z
dc.date.available2019-02-20T14:11:35Z
dc.date.issued2012en_US
dc.departmentDepartment of Computer Engineeringen_US
dc.description.abstractAvailability of an effective tool for protein multiple structural alignment (MSTA) is essential for discovery and analysis of biologically significant structural motifs that can help solve functional annotation and drug design problems. Existing MSTA methods collect residue correspondences mostly through pairwise comparison of consecutive fragments, which can lead to suboptimal alignments, especially when the similarity among the proteins is low. We introduce a novel strategy based on: building a contactwindow based motif library from the protein structural data, discovery and extension of common alignment seeds from this library, and optimal superimposition of multiple structures according to these alignment seeds by an enhanced partial order curve comparison method. The ability of our strategy to detect multiple correspondences simultaneously, to catch alignments globally, and to support flexible alignments, endorse a sensitive and robust automated algorithm that can expose similarities among protein structures even under low similarity conditions. Our method yields better alignment results compared to other popular MSTA methods, on several protein structure data sets that span various structural folds and represent different protein similarity levels. A web-based alignment tool, a downloadable executable, and detailed alignment results for the data sets used here are available at http://sacan.biomed. drexel.edu/Smolign and http://bio.cse.ohio-state.edu/Smolign.en_US
dc.identifier.doi10.1109/TCBB.2011.67en_US
dc.identifier.eissn1557-9964
dc.identifier.issn1545-5963
dc.identifier.urihttp://hdl.handle.net/11693/49625
dc.language.isoEnglishen_US
dc.publisherInstitute of Electrical and Electronics Engineersen_US
dc.relation.isversionofhttps://doi.org/10.1109/TCBB.2011.67en_US
dc.source.titleIEEE/ACM Transactions on Computational Biology and Bioinformaticsen_US
dc.subjectProtein structureen_US
dc.subjectMultiple structure alignmenten_US
dc.subjectPartial order curve comparisonen_US
dc.subjectStructural motif libraryen_US
dc.subjectSecondary structure elements (SSE)en_US
dc.subjectDistance mapen_US
dc.subjectContact mapen_US
dc.subjectHOMSTRADen_US
dc.titleSmolign: a spatial motifs-based protein multiple structural alignment methoden_US
dc.typeArticleen_US
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