ReviewMethods (San Diego, Calif.)2010
SHAPE-directed RNA secondary structure prediction.
Review in Methods (San Diego, Calif.), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 187 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
187 citing papers in PubMed.
- A Workflow for Identifying Helicase-Dependent RNA Structural Changes in Transcriptional Termination: From DMS Sequencing Analysis to Reporter Assay-Based Validation.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Thermodynamic prediction of RNA cellular activity from sequence via conformational ensembles.Cell · 2026Article
- Decoding the Structural Complexity of Viral RNAs with SHAPE to Guide Antiviral Therapeutics.Viruses · 2026Review
- RNA Aptamers and Epitranscriptomics: Charting Unexplored Territories in RNA Biology.Molecular diagnosis & therapy · 2026Review
- Structure and sequence characteristics of 5'-stem-loop 1 modulate the escape from nsp1-mediated repression in SARS-CoV-2 variants.Nucleic acids research · 2026Article
- Deep learning for RNA secondary structure determination: gauging generalizability and broadening the scope of traditional methods.RNA (New York, N.Y.) · 2026Review
- Mapping the RNA Chaperone Activity of the Trypanosoma brucei Editosome Using SHAPE-Chemical Probing.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Enhancing RNA 3D Structure Prediction in CASP16: Integrating Physics-Based Modeling With Machine Learning for Improved Predictions.Proteins · 2026Article
- Deep Learning for RNA Secondary Structure Determination: Gauging Generalizability and Broadening the Scope of Traditional Methods.bioRxiv : the preprint server for biology · 2025Article
- Structural analysis of the lncRNA SChLAP1 reveals protein binding interfaces and a conformationally heterogenous retroviral insertion.RNA (New York, N.Y.) · 2025Article
- Energy-Dependent Changes in Ion Mobility Peak Width Reveal Stability Shifts in Ribonucleic Acid Stem Loops.Journal of the American Society for Mass Spectrometry · 2025Article
- Defining the Parameters for Sorting of RNA Cargo Into Extracellular Vesicles.Journal of extracellular vesicles · 2025Article
- Sequential structure probing of cotranscriptional RNA folding intermediates.Nature communications · 2025Article
- A structural element within the 5'UTR of β-catenin mRNA modulates its translation under hypoxia.Nucleic acids research · 2025Article
- Circular PVT1 promotes cardiac fibroblast activation interacting with miR-30a-5p and miR-125b-5p.Cell death & disease · 2025Article
- Rapid folding of nascent RNA regulates eukaryotic RNA biogenesis.Molecular cell · 2025Article
- IPANEMAP Suite: a pipeline for probing-informed RNA structure modeling.NAR genomics and bioinformatics · 2025Article
- SHAPE Probing to Screen Computationally Designed RNA.Methods in molecular biology (Clifton, N.J.) · 2025Article
- DHX36 binding induces RNA structurome remodeling and regulates RNA abundance via mNature communications · 2024Article
- Identification of RNA structures and their roles in RNA functions.Nature reviews. Molecular cell biology · 2024Review
127 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
2 authors.
Funding
Abstract
The diverse functional roles of RNA are determined by its underlying structure. Accurate and comprehensive knowledge of RNA structure would inform a broader understanding of RNA biology and facilitate exploiting RNA as a biotechnological tool and therapeutic target. Determining the pattern of base pairing, or secondary structure, of RNA is a first step in these endeavors. Advances in experimental, computational, and comparative analysis approaches for analyzing secondary structure have yielded accurate structures for many small RNAs, but only a few large (>500 nts) RNAs. In addition, most current methods for determining a secondary structure require considerable effort, analytical expertise, and technical ingenuity. In this review, we outline an efficient strategy for developing accurate secondary structure models for RNAs of arbitrary length. This approach melds structural information obtained using SHAPE chemistry with structure prediction using nearest-neighbor rules and the dynamic programming algorithm implemented in the RNAstructure program. Prediction accuracies reach >or=95% for RNAs on the kilobase scale. This approach facilitates both development of new models and refinement of existing RNA structure models, which we illustrate using the Gag-Pol frameshift element in an HIV-1 M-group genome. Most promisingly, integrated experimental and computational refinement brings closer the ultimate goal of efficiently and accurately establishing the secondary structure for any RNA sequence.
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.