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

    Author(s)
    Zhang, Wei
    Dunker, A Keith
    Zhou, Yaoqi
    Griffith University Author(s)
    Zhou, Yaoqi
    Year published
    2008
    Metadata
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    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, ...
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    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
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    Journal Title
    Proteins: Structure, Function, and Bioinformatics
    Volume
    71
    Issue
    1
    DOI
    https://doi.org/10.1002/prot.21654
    Subject
    Mathematical sciences
    Biological sciences
    Information and computing sciences
    Publication URI
    http://hdl.handle.net/10072/57572
    Collection
    • Journal articles

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