RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme
By Zhichao Miao, Ryszard W. Adamiak, Maciej Antczak, R. Batey, Alexander J Becka, Marcin Biesiada, Michal J. Boniecki, Janusz M. Bujnicki, Shi-Jie Chen, C. Cheng and 36 more. 2017
197 citations recorded by the source corpus.
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 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 a notable need for an algorithm of improvement. All prediction models and assessment results are available at http://ahsoka.u-strasbg.fr/rnapuzzles/.
Subfields: Molecular Biology
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In Molecular Biology
- Rhiju Das
- Yaoqi Zhou
- Janusz M. Bujnicki
- Eric Westhof
- N. V. Dokholyan
- Andrew M. Watkins
- Jack Hanson
- Kuldip K. Paliwal
Citations in the corpus
- RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning (2019, methodology): “The usefulness of 2D structure prediction for 3D structure modeling has been demonstrated in RNA Puzzles (blind RNA structure prediction) 53 .”
- The HDOCK server for integrated protein–protein docking (2020, background): “CAUTION The RNA/DNA 3D structure prediction is still in the developing stage 101,102 .”
- Using Rosetta for RNA homology modeling (2019, methodology): “Recent blind modeling challenges in the RNA Puzzles trials (Miao et al., 2017) support the view that RNA homology modeling can be accurate and biologically useful.”
- FARFAR2: Improved de novo Rosetta prediction of complex global RNA folds (2020, unknown): “Through our participation in the RNA-Puzzles trials (Cruz et al., 2012; Miao et al., 2015, 2017), we have kept records of our strategies for each prediction challenge, including secondary structure predictions, inferences based on homology to prior deposited structures, and functional constraints,…”