RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction

  1. Eric Westhof1,17
  1. 1Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC-CNRS, F-67084 Strasbourg, France
  2. 2Institute for Research in Immunology and Cancer (IRIC), Department of Computer Science and Operations Research, Université de Montréal, Montréal, Québec H3C 3J7, Canada
  3. 3Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
  4. 4Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland
  5. 5Department of Physics and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA
  6. 6Department of Biochemistry,
  7. 7Department of Physics, Stanford University, Stanford, California 94305, USA
  8. 8Department of Biochemistry and Biophysics, University of North Carolina, School of Medicine, Chapel Hill, North Carolina 27599, USA
  9. 9Computational & Systems Biology Program, Institute for Cell and Molecular Biology, Uppsala University, 751 05 Uppsala, Sweden
  10. 10Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA
  11. 11Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
  12. 12Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
  13. 13DNA Software, Ann Arbor, Michigan 48104, USA
  14. 14Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, USA
  15. 15Max F. Perutz Laboratories, Department of Biochemistry, University of Vienna, Vienna 1030, Austria
  16. 16Department of Chemistry and Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, Ohio 43403, USA

    Abstract

    We report the results of a first, collective, blind experiment in RNA three-dimensional (3D) structure prediction, encompassing three prediction puzzles. The goals are to assess the leading edge of RNA structure prediction techniques; compare existing methods and tools; and evaluate their relative strengths, weaknesses, and limitations in terms of sequence length and structural complexity. The results should give potential users insight into the suitability of available methods for different applications and facilitate efforts in the RNA structure prediction community in ongoing efforts to improve prediction tools. We also report the creation of an automated evaluation pipeline to facilitate the analysis of future RNA structure prediction exercises.

    Keywords

    Footnotes

    • Received October 22, 2011.
    • Accepted December 20, 2011.

    Freely available online through the RNA Open Access option.

    | Table of Contents
    OPEN ACCESS ARTICLE

    This Article

    1. Published in Advance February 23, 2012, doi: 10.1261/rna.031054.111 RNA 18: 610-625 Copyright © 2012 RNA Society

    Article Category

    Share

    Current Issue

    1. May 2024, 30 (5)
    1. Current Issue
    1. Alert me to new issues of RNA