ArticleNucleic acids research2011
ModeRNA: a tool for comparative modeling of RNA 3D structure.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 159 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
159 citing papers in PubMed.
- Crosstalk between RNA secondary and three-dimensional structure prediction: a comprehensive study.RNA biology · 2026Article
- RAFA: RNA all-atom structure reconstruction from sparse anchor coordinates.Bioinformatics (Oxford, England) · 2026Article
- How Medically Important Antimicrobials Bind to the 30S Ribosomal Subunit in a Bacterial Pathogen.Biochemistry · 2026Article
- RNAbpFlow: base pair-augmented SE(3) flow matching for conditional RNA 3D structure generation.Nature methods · 2026Article
- Riboswitch-targeted improvement of lysine production in Bacillus and Priestia species.NPJ science of food · 2026Article
- Three-metal-ion catalysis by ribonuclease P holoenzyme: a new mechanistic insight into transfer RNA maturation.Research square · 2026Article
- The RNA promoter for pathogenic orthoflaviviruses replication is universal and serves as target for viral inhibition.PLoS pathogens · 2026Article
- Structural basis for protein-free catalysis by ribonuclease P ribozyme.Nature communications · 2026Article
- Structural investigation of human U6 snRNA recognition by spliceosomal recycling factor SART3 RNA recognition motifs.The FEBS journal · 2026Article
- Computational approaches for RNA structure prediction and design.Cell reports. Physical science · 2026Article
- gCoSRNA: Generalizable Coaxial Stacking Prediction for RNA Junctions Using Secondary Structure.Biomolecules · 2026Article
- DRfold2 is a deep learning-based tool that enables efficient and accurate RNA structure prediction.PLoS biology · 2026Article
- Quality assessment of RNA 3D structure models using deep learning and intermediate 2D maps.Communications biology · 2026Article
- Decoding RNA triple helices: identification from sequence and secondary structure.Briefings in bioinformatics · 2026Article
- Structure Modeling Protocols for Protein Multimer and RNA in CASP16 With Enhanced MSAs, Model Ranking, and Deep Learning.Proteins · 2026Article
- Integrating Magnetic Bead-Based SELEX withACS omega · 2025Article
- GMFOLD: Subgraph matching for high-throughput DNA-aptamer secondary structure classification and machine learning interpretability.Mathematical biosciences · 2025Article
- Structure of fungal tRNA ligase Trl1 with RNA reveals conserved substrate-binding principles.Nature structural & molecular biology · 2025Article
- RNAbpFlow: Base pair-augmented SE(3)-flow matching for conditional RNA 3D structure generation.bioRxiv : the preprint server for biology · 2025Article
- Has AlphaFold3 achieved success for RNA?Acta crystallographica. Section D, Structural biology · 2025Article
99 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
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA is a large group of functionally important biomacromolecules. In striking analogy to proteins, the function of RNA depends on its structure and dynamics, which in turn is encoded in the linear sequence. However, while there are numerous methods for computational prediction of protein three-dimensional (3D) structure from sequence, with comparative modeling being the most reliable approach, there are very few such methods for RNA. Here, we present ModeRNA, a software tool for comparative modeling of RNA 3D structures. As an input, ModeRNA requires a 3D structure of a template RNA molecule, and a sequence alignment between the target to be modeled and the template. It must be emphasized that a good alignment is required for successful modeling, and for large and complex RNA molecules the development of a good alignment usually requires manual adjustments of the input data based on previous expertise of the respective RNA family. ModeRNA can model post-transcriptional modifications, a functionally important feature analogous to post-translational modifications in proteins. ModeRNA can also model DNA structures or use them as templates. It is equipped with many functions for merging fragments of different nucleic acid structures into a single model and analyzing their geometry. Windows and UNIX implementations of ModeRNA with comprehensive documentation and a tutorial are freely available.
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.