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RNA. 2015 Jun;21(6):1066-84. doi: 10.1261/rna.049502.114. Epub 2015 Apr 16.

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures.

Author information

1
Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 67000 Strasbourg, France.
2
Department of Structural Chemistry and Biology of Nucleic Acids, Structural Chemistry of Nucleic Acids Laboratory, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.
3
Institute for Research in Immunology and Cancer (IRIC), Department of Computer Science and Operations Research, Université de Montréal, Montréal, Québec, Canada H3C 3J7.
4
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland.
5
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland.
6
Department of Physics and Astronomy, Department of Biochemistry, and Informatics Institute, University of Missouri-Columbia, Columbia, Missouri 65211, USA.
7
Department of Physics, Stanford University, Stanford, California 94305, USA.
8
National Heart, Lung and Blood Institute, Bethesda, Maryland 20892-8012, USA.
9
Department of Physics and Astronomy, College of Engineering and Science, Clemson University, Clemson, South Carolina 29634, USA.
10
Department of Biochemistry and Biophysics, University of North Carolina, School of Medicine, Chapel Hill, North Carolina 27599, USA.
11
Génétique Moléculaire Génomique Microbiologie, Institut de physiologie et de la chimie biologique, 67084 Strasbourg, France.
12
Institut de génétique et de biologie moléculaire et cellulaire, 67400 Strasbourg, France.
13
Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA.
14
Poznan University of Technology, Institute of Computing Science, 60-965 Poznan, Poland.
15
Department of Physics, Huazhong University of Science and Technology, 430074 Wuhan, China.

Abstract

This paper is a report of a second round of RNA-Puzzles, a collective and blind experiment in three-dimensional (3D) RNA structure prediction. Three puzzles, Puzzles 5, 6, and 10, represented sequences of three large RNA structures with limited or no homology with previously solved RNA molecules. A lariat-capping ribozyme, as well as riboswitches complexed to adenosylcobalamin and tRNA, were predicted by seven groups using RNAComposer, ModeRNA/SimRNA, Vfold, Rosetta, DMD, MC-Fold, 3dRNA, and AMBER refinement. Some groups derived models using data from state-of-the-art chemical-mapping methods (SHAPE, DMS, CMCT, and mutate-and-map). The comparisons between the predictions and the three subsequently released crystallographic structures, solved at diffraction resolutions of 2.5-3.2 Å, were carried out automatically using various sets of quality indicators. The comparisons clearly demonstrate the state of present-day de novo prediction abilities as well as the limitations of these state-of-the-art methods. All of the best prediction models have similar topologies to the native structures, which suggests that computational methods for RNA structure prediction can already provide useful structural information for biological problems. However, the prediction accuracy for non-Watson-Crick interactions, key to proper folding of RNAs, is low and some predicted models had high Clash Scores. These two difficulties point to some of the continuing bottlenecks in RNA structure prediction. All submitted models are available for download at http://ahsoka.u-strasbg.fr/rnapuzzles/.

KEYWORDS:

3D prediction; X-ray structures; bioinformatics; force fields; models; structure quality

PMID:
25883046
PMCID:
PMC4436661
DOI:
10.1261/rna.049502.114
[Indexed for MEDLINE]
Free PMC Article

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