RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures
Author:
Miao Zhichao, Adamiak Ryszard W., Blanchet Marc-Frédérick, Boniecki Michal, Bujnicki Janusz M., Chen Shi-Jie, Cheng Clarence, Chojnowski Grzegorz, Chou Fang-Chieh, Cordero Pablo, Cruz José Almeida, Ferré-D'Amaré Adrian R., Das Rhiju, Ding Feng, Dokholyan Nikolay V., Dunin-Horkawicz Stanislaw, Kladwang Wipapat, Krokhotin Andrey, Lach Grzegorz, Magnus Marcin, Major François, Mann Thomas H., Masquida Benoît, Matelska Dorota, Meyer Mélanie, Peselis Alla, Popenda Mariusz, Purzycka Katarzyna J., Serganov Alexander, Stasiewicz Juliusz, Szachniuk Marta, Tandon Arpit, Tian Siqi, Wang Jian, Xiao Yi, Xu Xiaojun, Zhang Jinwei, Zhao Peinan, Zok Tomasz, Westhof EricORCID
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/.
Funder
French Government French National Research Agency National Institutes of Health NIH Burroughs-Wellcome Foundation Bio-X HHMI Stanford Graduate Fellowship Conacyt fellowship European Research Council Foundation for Polish Science European Commission Polish National Science Centre Polish Ministry of Science and Higher Education NYU Whitehead fellowship Intramural Program of the National Heart, Lung and Blood Institute-NIH
Publisher
Cold Spring Harbor Laboratory
Subject
Molecular Biology
Cited by
156 articles.
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