Assessing secondary structure assignment of protein structures by using pairwise sequence-alignment benchmarks

Wei Zhang, A. Dunker, Yaoqi Zhou

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

How 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.

Original languageEnglish
Pages (from-to)61-67
Number of pages7
JournalProteins: Structure, Function and Genetics
Volume71
Issue number1
DOIs
StatePublished - Apr 2008

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Secondary Protein Structure
Benchmarking
Sequence Alignment
Proteins
Electric sparks
Servers
Informatics
Oceans and Seas

Keywords

  • Alignment benchmarks
  • Protein structure prediction
  • Secondary structures

ASJC Scopus subject areas

  • Genetics
  • Structural Biology
  • Biochemistry

Cite this

Assessing secondary structure assignment of protein structures by using pairwise sequence-alignment benchmarks. / Zhang, Wei; Dunker, A.; Zhou, Yaoqi.

In: Proteins: Structure, Function and Genetics, Vol. 71, No. 1, 04.2008, p. 61-67.

Research output: Contribution to journalArticle

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