ArticleStructure (London, England : 1993)2020
FARFAR2: Improved De Novo Rosetta Prediction of Complex Global RNA Folds.
Article in Structure (London, England : 1993), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 161 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
161 citing papers in PubMed.
- Crosstalk between RNA secondary and three-dimensional structure prediction: a comprehensive study.RNA biology · 2026Article
- dsRNAscan maps human dsRNAome, revealing conservation, intermolecular dsRNA, and correlates of ADAR dependency.Molecular cell · 2026Article
- The MODNAP benchmark set for modeling ribose-based modified nucleic acid and nucleic acid-protein complexes: a case study with AlphaFold 3.Nucleic acids research · 2026Article
- Hierarchical breakdown of RNA structure prediction in CASP16: from reliable local helices to speculative multimer assembly.Bioinformatics (Oxford, England) · 2026Article
- The trRosettaRNA server for RNA structure prediction.Nature protocols · 2026Review
- Fast activity prediction of chemically modified siRNAs via structure-based energy calculations and inference-augmented tabular deep learning.Molecular therapy. Nucleic acids · 2026Article
- Programmable Edge-to-Edge Assembly of RNA Nanostructures.ACS nano · 2026Article
- Characterizing RNA 3D structural features from DMS reactivity.Nucleic acids research · 2026Article
- Development of an RNA aptamer as a therapeutic agent for synucleinopathies.Nature communications · 2026Article
- Article
- RNAbpFlow: base pair-augmented SE(3) flow matching for conditional RNA 3D structure generation.Nature methods · 2026Article
- PlanarFold: a coarse-grained molecular dynamics model of RNA in two-dimensional space.Nature communications · 2026Article
- Geometric Deep Learning Reveals Ligandable and Cryptic RNA Binding Small Molecule Pockets (SMARTPocket).bioRxiv : the preprint server for biology · 2026Article
- Base modifications shift tertiary structure and activity in synthetic RNA origami and a natural ribozyme.Nature communications · 2026Article
- Detecting and quantifying overparametrization in RNA language models with REDIAL.bioRxiv : the preprint server for biology · 2026Article
- Multi-site DMS probing reveals higher-order structure of RNA-protein complexes in living cells.Molecular cell · 2026Article
- Inferring the qualities of protein-RNA models with graph transformers.Bioinformatics (Oxford, England) · 2026Article
- Exploring Secondary Structure Predictions for RNA-Targeted Drug Discovery: Power and Challenges.Journal of chemical information and modeling · 2026Article
- Spectral Graph Features for Reference-free RNA 3D Quality Assessment.bioRxiv : the preprint server for biology · 2026Article
- Aptamer-mediated modulation of PAI-1 function reveals a novel mechanism for restoring fibrinolytic balance.NAR molecular medicine · 2026Article
101 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
3 authors.
Funding
Abstract
Predicting RNA three-dimensional structures from sequence could accelerate understanding of the growing number of RNA molecules being discovered across biology. Rosetta's Fragment Assembly of RNA with Full-Atom Refinement (FARFAR) has shown promise in community-wide blind RNA-Puzzle trials, but lack of a systematic and automated benchmark has left unclear what limits FARFAR performance. Here, we benchmark FARFAR2, an algorithm integrating RNA-Puzzle-inspired innovations with updated fragment libraries and helix modeling. In 16 of 21 RNA-Puzzles revisited without experimental data or expert intervention, FARFAR2 recovers native-like structures more accurate than models submitted during the RNA-Puzzles trials. Remaining bottlenecks include conformational sampling for >80-nucleotide problems and scoring function limitations more generally. Supporting these conclusions, preregistered blind models for adenovirus VA-I RNA and five riboswitch complexes predicted native-like folds with 3- to 14 Å root-mean-square deviation accuracies. We present a FARFAR2 webserver and three large model archives (FARFAR2-Classics, FARFAR2-Motifs, and FARFAR2-Puzzles) to guide future applications and advances.
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.