RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction
- José Almeida Cruz1,
- Marc-Frédérick Blanchet2,
- Michal Boniecki3,
- Janusz M. Bujnicki3,4,
- Shi-Jie Chen5,
- Song Cao5,
- Rhiju Das6,7,
- Feng Ding8,
- Nikolay V. Dokholyan8,
- Samuel Coulbourn Flores9,
- Lili Huang10,
- Christopher A. Lavender11,
- Véronique Lisi2,
- François Major2,
- Katarzyna Mikolajczak3,
- Dinshaw J. Patel10,
- Anna Philips3,4,
- Tomasz Puton4,
- John Santalucia12,13,
- Fredrick Sijenyi13,
- Thomas Hermann14,
- Kristian Rother4,
- Magdalena Rother4,
- Alexander Serganov10,
- Marcin Skorupski4,
- Tomasz Soltysinski3,
- Parin Sripakdeevong6,7,
- Irina Tuszynska3,
- Kevin M. Weeks11,
- Christina Waldsich15,
- Michael Wildauer15,
- Neocles B. Leontis16 and
- Eric Westhof1,17
- 1Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC-CNRS, F-67084 Strasbourg, France
- 2Institute for Research in Immunology and Cancer (IRIC), Department of Computer Science and Operations Research, Université de Montréal, Montréal, Québec H3C 3J7, Canada
- 3Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
- 4Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland
- 5Department of Physics and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA
- 6Department of Biochemistry,
- 7Department of Physics, Stanford University, Stanford, California 94305, USA
- 8Department of Biochemistry and Biophysics, University of North Carolina, School of Medicine, Chapel Hill, North Carolina 27599, USA
- 9Computational & Systems Biology Program, Institute for Cell and Molecular Biology, Uppsala University, 751 05 Uppsala, Sweden
- 10Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA
- 11Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- 12Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
- 13DNA Software, Ann Arbor, Michigan 48104, USA
- 14Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, USA
- 15Max F. Perutz Laboratories, Department of Biochemistry, University of Vienna, Vienna 1030, Austria
- 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
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↵17 Corresponding author.
E-mail E.Westhof{at}ibmc-cnrs.unistra.fr.
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Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.031054.111.
- Received October 22, 2011.
- Accepted December 20, 2011.
- Copyright © 2012 RNA Society
Freely available online through the RNA Open Access option.