Assessment of CASP6 predictions for new and nearly new fold targets

Authors

  • James J. Vincent,

    1. Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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  • Chin-Hsien Tai,

    1. Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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  • B.K. Sathyanarayana,

    Corresponding author
    1. Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
    • Bldg. 37, Rm. 5120, National Institutes of Health, 37 Convent Drive MSC 4264, Bethesda MD 20892-4264
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  • Byungkook Lee

    1. Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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  • This article is a US Government work and, as such, is in the public domain in the United States of America.

  • This article was originally published onine as an accepted preprint. The “Published Online” date corresponds to the preprint version.

Abstract

This is a report of the assessment of the predictions made for the CASP6 protein structure prediction experiment conducted in 2004 in the New Fold (NF) category. There were nine protein domains that were judged to have new folds (NF) and 16 for which a similar structure was known but the sequence similarity was judged to be too low for them to be easily recognized (FR/A). We selected all NF targets and eight of the 16 FR/A targets judged to be at the borderline between NF and FR/A for evaluation in the NF category. A total of 165 prediction groups submitted over 7400 structural models for these targets. The quality of these models was evaluated using the GDT_TS scores of the structural similarity detection program LGA and by visual inspection of the top-scoring models. The best models submitted bore an overall similarity to the target structure for three or four of the nine NF targets and for all but one of the FR/A targets. High-scoring models for the NF targets were submitted by several different groups. When both the NF and FR/A targets were considered, Baker group dominated by submitting best models for seven of the 17 targets, but 14 other groups also managed to submit best models for one or more targets. Proteins 2005;Suppl 7:67–83. © 2005 Wiley-Liss, Inc.

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