Show simple item record

dc.contributor.authorZhang, Wei
dc.contributor.authorDunker, A Keith
dc.contributor.authorZhou, Yaoqi
dc.date.accessioned2017-05-03T15:56:00Z
dc.date.available2017-05-03T15:56:00Z
dc.date.issued2008
dc.date.modified2014-03-31T23:38:00Z
dc.identifier.issn0887-3585
dc.identifier.doi10.1002/prot.21654
dc.identifier.urihttp://hdl.handle.net/10072/57572
dc.description.abstractHow to make an objective assignment of secondary structures based on a protein structure is an unsolved problem. Defining the boundaries between helix, sheet, and coil structures is arbitrary, and commonly accepted standard assignments do not exist. Here, we propose a criterion that assesses secondary structure assignment based on the similarity of the secondary structures assigned to pairwise sequence-alignment benchmarks, where these benchmarks are determined by prior structural alignments of the protein pairs. This criterion is used to rank six secondary structure assignment methods: STRIDE, DSSP, SECSTR, KAKSI, P-SEA, and SEGNO with three established sequence-alignment benchmarks (PREFAB, SABmark, and SALIGN). STRIDE and KAKSI achieve comparable success rates in assigning the same secondary structure elements to structurally aligned residues in the three benchmarks. Their success rates are between 1-4% higher than those of the other four methods. The consensus of STRIDE, KAKSI, SECSTR, and P-SEA, called SKSP, improves assignments over the best single method in each benchmark by an additional 1%. These results support the usefulness of the sequence-alignment benchmarks as a means to evaluate secondary structure assignment. The SKSP server and the benchmarks can be accessed at http://sparks.informatics.iupui.edu
dc.description.peerreviewedYes
dc.description.publicationstatusYes
dc.languageEnglish
dc.language.isoeng
dc.publisherWiley-Liss
dc.publisher.placeUnited States
dc.relation.ispartofstudentpublicationN
dc.relation.ispartofpagefrom61
dc.relation.ispartofpageto67
dc.relation.ispartofissue1
dc.relation.ispartofjournalProteins: Structure, Function, and Bioinformatics
dc.relation.ispartofvolume71
dc.rights.retentionY
dc.subject.fieldofresearchMathematical sciences
dc.subject.fieldofresearchBiological sciences
dc.subject.fieldofresearchInformation and computing sciences
dc.subject.fieldofresearchcode49
dc.subject.fieldofresearchcode31
dc.subject.fieldofresearchcode46
dc.titleAssessing secondary structure assignment of protein structures by using pairwise sequence-alignment benchmarks
dc.typeJournal article
dc.type.descriptionC1 - Articles
dc.type.codeC - Journal Articles
gro.date.issued2008
gro.hasfulltextNo Full Text
gro.griffith.authorZhou, Yaoqi


Files in this item

FilesSizeFormatView

There are no files associated with this item.

This item appears in the following Collection(s)

  • Journal articles
    Contains articles published by Griffith authors in scholarly journals.

Show simple item record