ArticleRNA (New York, N.Y.)2015
RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures.
Article in RNA (New York, N.Y.), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 126 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
126 citing papers in PubMed, 205 citations in OpenAlex.
- Crosstalk between RNA secondary and three-dimensional structure prediction: a comprehensive study.RNA biology · 2026Article
- Recent Advances in Chemical Probing Strategies for RNA Structure Determination In Vivo.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Review
- FRET-guided selection of RNA 3D structures.Nucleic acids research · 2026Article
- Computational approaches for RNA structure prediction and design.Cell reports. Physical science · 2026Article
- TiRNA: a coarse-grained method with temperature and ion effects for RNA structure folding and prediction.Nucleic acids research · 2026Article
- Enhancing RNA 3D Structure Prediction in CASP16: Integrating Physics-Based Modeling With Machine Learning for Improved Predictions.Proteins · 2026Article
- Assessment of Nucleic Acid Structure Prediction in CASP16.Proteins · 2026Article
- Structure Modeling Protocols for Protein Multimer and RNA in CASP16 With Enhanced MSAs, Model Ranking, and Deep Learning.Proteins · 2026Article
- The RNA-Puzzles Assessments of RNA-Only Targets in CASP16.Proteins · 2026Article
- Predicting RNA Structure Utilizing Attention from Pretrained Language Models.Journal of chemical information and modeling · 2025Article
- Assessment of nucleic acid structure prediction in CASP16.bioRxiv : the preprint server for biology · 2025Article
- Has AlphaFold3 achieved success for RNA?Acta crystallographica. Section D, Structural biology · 2025Article
- RNA-Puzzles Round V: blind predictions of 23 RNA structures.Nature methods · 2025Article
- NuFold: end-to-end approach for RNA tertiary structure prediction with flexible nucleobase center representation.Nature communications · 2025Article
- A virtual system-coupled molecular dynamics simulation free from experimental knowledge on binding sites: Application to RNA-ligand binding free-energy landscape.Biophysics and physicobiology · 2025Article
- RNA-TorsionBERT: leveraging language models for RNA 3D torsion angles prediction.Bioinformatics (Oxford, England) · 2024Article
- Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction.PLoS computational biology · 2024Article
- Accurate RNA 3D structure prediction using a language model-based deep learning approach.Nature methods · 2024Article
- RNAtango: Analysing and comparing RNA 3D structures via torsional angles.PLoS computational biology · 2024Article
- Machine learning in RNA structure prediction: Advances and challenges.Biophysical journal · 2024Review
66 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
40 authors at 14 institutions in 5 countries.
Funding
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/.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.