Miao Z, Adamiak R W, Antczak M, Batey R T, Becka A J, Biesiada M, Boniecki M J, Bujnicki J, Chen S J, Cheng C Y, Chou F C, Ferré-D'Amaré A R, Das R, Dawson W K, Feng D, Dokholyan N V, Dunin-Horkawicz S, Geniesse C, Kappel K, Kladwang W, Krokhotin A, Lach G E, Major F, Mann T H, Magnus M, Pachulska-Wieczorek K, Patel D J, Piccirilli J A, Popenda M, Purzycka K J, Ren A, Rice G M, Santalucia Jr. J, Sarzynska J, Szachniuk M, Tandon A, Trausch J J, Tian S, Wang J, Weeks K M, 2nd. B Williams, Xiao Y, Xu X, Zhang D, Zok T, Westhof E
RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. Article de journal
Dans: RNA, vol. 23, no. 5, p. 655-672, 2017, ISBN: 28138060.
Résumé | Liens | BibTeX | Étiquettes: 3D prediction X-ray structures bioinformatics force fields models structure quality, Unité ARN, WESTHOF
@article{,
title = {RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme.},
author = {Z Miao and R W Adamiak and M Antczak and R T Batey and A J Becka and M Biesiada and M J Boniecki and J Bujnicki and S J Chen and C Y Cheng and F C Chou and A R Ferré-D'Amaré and R Das and W K Dawson and D Feng and N V Dokholyan and S Dunin-Horkawicz and C Geniesse and K Kappel and W Kladwang and A Krokhotin and G E Lach and F Major and T H Mann and M Magnus and K Pachulska-Wieczorek and D J Patel and J A Piccirilli and M Popenda and K J Purzycka and A Ren and G M Rice and Jr. J Santalucia and J Sarzynska and M Szachniuk and A Tandon and J J Trausch and S Tian and J Wang and K M Weeks and 2nd. B Williams and Y Xiao and X Xu and D Zhang and T Zok and E Westhof},
url = {https://www.ncbi.nlm.nih.gov/pubmed/28138060?dopt=Abstract},
doi = {10.1261/rna.060368.116},
isbn = {28138060},
year = {2017},
date = {2017-01-01},
journal = {RNA},
volume = {23},
number = {5},
pages = {655-672},
abstract = {RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch aptamers and puzzle 7, a ribozyme structure, are included in this round of the experiment. The riboswitch structures include biological binding sites for small molecules (S-adenosyl methionine, cyclic diadenosine monophosphate, 5-amino 4-imidazole carboxamide riboside 5'-triphosphate, glutamine) and proteins (YbxF) and one set describes large conformational changes between ligand-free and ligand-bound states; the Varkud satellite ribozyme is the most recently solved structure of a known large ribozyme. All the puzzles have established biological functions and require structural understanding to appreciate their molecular mechanisms. Through the use of fast-track experimental data, including multidimensional chemical mapping, and accurate prediction of RNA secondary structure, a large portion of the contacts in 3D have been predicted correctly leading to similar topologies for the top ranking predictions. Template-based and homology-derived predictions could predict structures to particularly high accuracies. However, achieving biological insights from de novo prediction of RNA 3D structures still depends on the size and complexity of the RNA. Blind computational predictions of RNA structures already appear to provide useful structural information in many cases. Similar to the previous RNA-Puzzles Round II experiment, the prediction of non-Watson-Crick interactions and the observed high atomic clash scores reveal notable need for algorithm of improvement. All prediction models and assessment results are available at http://ahsoka.u-strasbg.fr/rnapuzzles/.},
keywords = {3D prediction X-ray structures bioinformatics force fields models structure quality, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Miao Z, Adamiak R W, Blanchet M F, Boniecki M, Bujnicki J M, Chen S J, Cheng C, Chojnowski G, Chou F C, Cordero P, Cruz J A, Ferré-D'amaré A R, Das R, Ding F, Dokholyan N V, Dunin-Horkawicz S, Kladwang W, Krokhotin A, Lach G, Magnus M, Major F, Mann T H, Masquida B, Matelska D, Meyer M, Peselis A, Popenda M, Purzycka K J, Serganov A, Stasiewicz J, Szachniuk M, Tandon A, Tian S, Wang J, Xiao Y, Xu X, Zhang J, Zhao P, Zok T, Westhof E
RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures. Article de journal
Dans: RNA, vol. 21, no. 6, p. 1066-1084, 2015, ISBN: 25883046.
Résumé | Liens | BibTeX | Étiquettes: 3D prediction X-ray structures bioinformatics force fields models structure quality, Unité ARN, WESTHOF
@article{,
title = {RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures.},
author = {Z Miao and R W Adamiak and M F Blanchet and M Boniecki and J M Bujnicki and S J Chen and C Cheng and G Chojnowski and F C Chou and P Cordero and J A Cruz and A R Ferré-D'amaré and R Das and F Ding and N V Dokholyan and S Dunin-Horkawicz and W Kladwang and A Krokhotin and G Lach and M Magnus and F Major and T H Mann and B Masquida and D Matelska and M Meyer and A Peselis and M Popenda and K J Purzycka and A Serganov and J Stasiewicz and M Szachniuk and A Tandon and S Tian and J Wang and Y Xiao and X Xu and J Zhang and P Zhao and T Zok and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25883046},
doi = {10.1261/rna.049502.114},
isbn = {25883046},
year = {2015},
date = {2015-01-01},
journal = {RNA},
volume = {21},
number = {6},
pages = {1066-1084},
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, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}