Assessment of predictions submitted for the CASP7 domain prediction category

    Authors

    M. Tress; J. Cheng; P. Baldi; K. Joo; J. Lee; J. H. Seo; J. Lee; D. Baker; D. Chivian; D. Kim;L. Ezkurdia

    Comments

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    Abbreviated Journal Title

    Proteins

    Keywords

    domain boundaries; domain overlap; evaluation; ab initio domain; prediction; template-based domain prediction; proteins; SECONDARY STRUCTURE; PROTEIN STRUCTURES; NEURAL-NETWORKS; DATABASE; INFORMATION; GENERATION; BOUNDARIES; SEQUENCES; SELECTION; ALIGNMENT; Biochemistry & Molecular Biology; Biophysics

    Abstract

    This paper details the assessment process and evaluation results for the Critical Assessment of Protein Structure Prediction (CASP7) domain prediction category. Domain predictions were assessed using the Normalized Domain Overlap score introduced in CASP6 and the accuracy of prediction of domain break points. The results of the analysis clearly demonstrate that the best methods are able to make consistently reliable predictions when the target has a structural template, although they are less good when the domain break occurs in a region not covered by a template. The conditions of the experiment meant that it was impossible to draw any conclusions about domain prediction for free modeling targets and it was also difficult to draw many distinctions between the best groups. Two thirds of the targets submitted were single domains and hence regarded as easy to predict. Even those targets defined as having multiple domains always had at least one domain with a similar template structure.

    Journal Title

    Proteins-Structure Function and Bioinformatics

    Volume

    69

    Publication Date

    1-1-2007

    Document Type

    Article; Proceedings Paper

    Language

    English

    First Page

    137

    Last Page

    151

    WOS Identifier

    WOS:000251502400015

    ISSN

    0887-3585

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