CASP6 data processing and automatic evaluation at the protein structure prediction center

Authors

  • Andriy Kryshtafovych,

    1. Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, California
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  • Maciej Milostan,

    1. Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, California
    Current affiliation:
    1. Institute of Computing Science, Poznan University of Technology, Poznan, Poland
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  • Lukasz Szajkowski,

    1. Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, California
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  • Pawel Daniluk,

    1. Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, California
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  • Krzysztof Fidelis

    Corresponding author
    1. Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, California
    • Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, CA 94551
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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 online as an accepted preprint. The “Published Online” date corresponds to the preprint version.

Abstract

We present a short overview of the system governing data processing and automatic evaluation of predictions in CASP6, implemented at the Livermore Protein Structure Prediction Center. The system incorporates interrelated facilities for registering participants, collecting prediction targets from crystallographers and NMR spectroscopists and making them available to the CASP6 participants, accepting predictions and providing their preliminary evaluation, and finally, storing and visualizing results. We have automatically evaluated predictions submitted to CASP6 using criteria and methods developed over the successive CASP experiments. Also, we have tested a new evaluation technique based on non-rigid-body type superpositions. Approximately the same number of predictions has been submitted to CASP6 as to all previous CASPs combined, making navigation through and understanding of the data particularly challenging. To facilitate this, we have substantially modernized all data handling procedures, including implementation of a dedicated relational database. An overview of our redesigned website is also presented (http://predictioncenter.org/casp6/). Proteins 2005;Suppl 7:19–23. © 2005 Wiley-Liss, Inc.

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