title: RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures.
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/.
authors.affiliation: Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 67000 Strasbourg, France.
authors.forename: Zhichao
authors.initials: Z
authors.lastname: Miao
authors.affiliation: 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.
authors.forename: Ryszard W
authors.initials: RW
authors.lastname: Adamiak
authors.affiliation: Institute for Research in Immunology and Cancer (IRIC), Department of Computer Science and Operations Research, Université de Montréal, Montréal, Québec, Canada H3C 3J7.
authors.forename: Marc-Frédérick
authors.initials: MF
authors.lastname: Blanchet
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland.
authors.forename: Michal
authors.initials: M
authors.lastname: Boniecki
authors.affiliation: 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.
authors.forename: Janusz M
authors.initials: JM
authors.lastname: Bujnicki
authors.affiliation: Department of Physics and Astronomy, Department of Biochemistry, and Informatics Institute, University of Missouri-Columbia, Columbia, Missouri 65211, USA.
authors.forename: Shi-Jie
authors.initials: SJ
authors.lastname: Chen
authors.affiliation: Department of Physics, Stanford University, Stanford, California 94305, USA.
authors.forename: Clarence
authors.initials: C
authors.lastname: Cheng
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland.
authors.forename: Grzegorz
authors.initials: G
authors.lastname: Chojnowski
authors.affiliation: Department of Physics, Stanford University, Stanford, California 94305, USA.
authors.forename: Fang-Chieh
authors.initials: FC
authors.lastname: Chou
authors.affiliation: Department of Physics, Stanford University, Stanford, California 94305, USA.
authors.forename: Pablo
authors.initials: P
authors.lastname: Cordero
authors.affiliation: Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 67000 Strasbourg, France.
authors.forename: José Almeida
authors.initials: JA
authors.lastname: Cruz
authors.affiliation: National Heart, Lung and Blood Institute, Bethesda, Maryland 20892-8012, USA.
authors.forename: Adrian R
authors.initials: AR
authors.lastname: Ferré-D'Amaré
authors.affiliation: Department of Physics, Stanford University, Stanford, California 94305, USA.
authors.forename: Rhiju
authors.initials: R
authors.lastname: Das
authors.affiliation: Department of Physics and Astronomy, College of Engineering and Science, Clemson University, Clemson, South Carolina 29634, USA.
authors.forename: Feng
authors.initials: F
authors.lastname: Ding
authors.affiliation: Department of Biochemistry and Biophysics, University of North Carolina, School of Medicine, Chapel Hill, North Carolina 27599, USA.
authors.forename: Nikolay V
authors.initials: NV
authors.lastname: Dokholyan
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland.
authors.forename: Stanislaw
authors.initials: S
authors.lastname: Dunin-Horkawicz
authors.affiliation: Department of Physics, Stanford University, Stanford, California 94305, USA.
authors.forename: Wipapat
authors.initials: W
authors.lastname: Kladwang
authors.affiliation: Department of Biochemistry and Biophysics, University of North Carolina, School of Medicine, Chapel Hill, North Carolina 27599, USA.
authors.forename: Andrey
authors.initials: A
authors.lastname: Krokhotin
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland.
authors.forename: Grzegorz
authors.initials: G
authors.lastname: Lach
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland.
authors.forename: Marcin
authors.initials: M
authors.lastname: Magnus
authors.affiliation: Institute for Research in Immunology and Cancer (IRIC), Department of Computer Science and Operations Research, Université de Montréal, Montréal, Québec, Canada H3C 3J7.
authors.forename: François
authors.initials: F
authors.lastname: Major
authors.affiliation: Department of Physics, Stanford University, Stanford, California 94305, USA.
authors.forename: Thomas H
authors.initials: TH
authors.lastname: Mann
authors.affiliation: Génétique Moléculaire Génomique Microbiologie, Institut de physiologie et de la chimie biologique, 67084 Strasbourg, France.
authors.forename: Benoît
authors.initials: B
authors.lastname: Masquida
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland.
authors.forename: Dorota
authors.initials: D
authors.lastname: Matelska
authors.affiliation: Institut de génétique et de biologie moléculaire et cellulaire, 67400 Strasbourg, France.
authors.forename: Mélanie
authors.initials: M
authors.lastname: Meyer
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA.
authors.forename: Alla
authors.initials: A
authors.lastname: Peselis
authors.affiliation: 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.
authors.forename: Mariusz
authors.initials: M
authors.lastname: Popenda
authors.affiliation: 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.
authors.forename: Katarzyna J
authors.initials: KJ
authors.lastname: Purzycka
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Serganov
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland.
authors.forename: Juliusz
authors.initials: J
authors.lastname: Stasiewicz
authors.affiliation: Poznan University of Technology, Institute of Computing Science, 60-965 Poznan, Poland.
authors.forename: Marta
authors.initials: M
authors.lastname: Szachniuk
authors.affiliation: Department of Biochemistry and Biophysics, University of North Carolina, School of Medicine, Chapel Hill, North Carolina 27599, USA.
authors.forename: Arpit
authors.initials: A
authors.lastname: Tandon
authors.affiliation: Department of Physics, Stanford University, Stanford, California 94305, USA.
authors.forename: Siqi
authors.initials: S
authors.lastname: Tian
authors.affiliation: Department of Physics, Huazhong University of Science and Technology, 430074 Wuhan, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Physics, Huazhong University of Science and Technology, 430074 Wuhan, China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Xiao
authors.affiliation: Department of Physics and Astronomy, Department of Biochemistry, and Informatics Institute, University of Missouri-Columbia, Columbia, Missouri 65211, USA.
authors.forename: Xiaojun
authors.initials: X
authors.lastname: Xu
authors.affiliation: National Heart, Lung and Blood Institute, Bethesda, Maryland 20892-8012, USA.
authors.forename: Jinwei
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Department of Physics and Astronomy, Department of Biochemistry, and Informatics Institute, University of Missouri-Columbia, Columbia, Missouri 65211, USA.
authors.forename: Peinan
authors.initials: P
authors.lastname: Zhao
authors.affiliation: Poznan University of Technology, Institute of Computing Science, 60-965 Poznan, Poland.
authors.forename: Tomasz
authors.initials: T
authors.lastname: Zok
authors.affiliation: Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 67000 Strasbourg, France.
authors.forename: Eric
authors.identifier: http://orcid.org/0000-0002-6172-5422
authors.initials: E
authors.lastname: Westhof
mesh_terms: D019295:Computational Biology / Q000379:methods*; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012333:RNA, Messenger / Q000737:chemistry; D012343:RNA, Transfer / Q000737:chemistry; D012984:Software
chemical_list: D012333:RNA, Messenger; D012313:RNA; D012343:RNA, Transfer
keywords: 3D prediction; X-ray structures; bioinformatics; force fields; models; structure quality