ArticleRNA (New York, N.Y.)2014
RNA secondary structure modeling at consistent high accuracy using differential SHAPE.
Article in RNA (New York, N.Y.), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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Who cites it
61 citing papers in PubMed.
- Decoding the Structural Complexity of Viral RNAs with SHAPE to Guide Antiviral Therapeutics.Viruses · 2026Review
- Recent Advances in Chemical Probing Strategies for RNA Structure Determination In Vivo.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Review
- Decoding the lncRNA World: Comprehensive Approaches to lncRNA Structure and Interactome Studies.Cells · 2026Review
- Hierarchical analysis of RNA secondary structures with pseudoknots based on sections.PLoS computational biology · 2026Article
- Mapping the RNA Chaperone Activity of the Trypanosoma brucei Editosome Using SHAPE-Chemical Probing.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Accurate RNA 3D structure prediction using a language model-based deep learning approach.Nature methods · 2024Article
- Modeling the structure and DAP5-binding site of the FGF-9 5'-UTR RNA utilized in cap-independent translation.RNA (New York, N.Y.) · 2024Article
- Isoform-specific RNA structure determination using Nano-DMS-MaP.Nature protocols · 2024Review
- Article
- How Parameters Influence SHAPE-Directed Predictions.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Molecular Dynamics Simulations with Grand-Canonical Reweighting Suggest Cooperativity Effects in RNA Structure Probing Experiments.Journal of chemical theory and computation · 2023Article
- Structural analysis of MALAT1 long noncoding RNA in cells and in evolution.RNA (New York, N.Y.) · 2023Article
- The Evaluation of SHAPE-MaP RNA Structure Probing Protocols Reveals a Novel Role of MnInternational journal of molecular sciences · 2023Article
- Eukaryotic initiation factor 4F promotes a reorientation of eukaryotic initiation factor 3 binding on the 5' and the 3' UTRs of barley yellow dwarf virus mRNA.Nucleic acids research · 2022Article
- Progress toward SHAPE Constrained Computational Prediction of Tertiary Interactions in RNA Structure.Non-coding RNA · 2021Article
- CriTER-A: A Novel Temperature-Dependent Noncoding RNA Switch in the Telomeric Transcriptome ofInternational journal of molecular sciences · 2021Article
- Characteristic chemical probing patterns of loop motifs improve prediction accuracy of RNA secondary structures.Nucleic acids research · 2021Article
- In vivo structure of the Ty1 retrotransposon RNA genome.Nucleic acids research · 2021Article
- IsRNA1:Journal of chemical theory and computation · 2021Article
- On the Problem of Reconstructing a Mixture of RNA Structures.Bulletin of mathematical biology · 2020Article
1 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
RNA secondary structure modeling is a challenging problem, and recent successes have raised the standards for accuracy, consistency, and tractability. Large increases in accuracy have been achieved by including data on reactivity toward chemical probes: Incorporation of 1M7 SHAPE reactivity data into an mfold-class algorithm results in median accuracies for base pair prediction that exceed 90%. However, a few RNA structures are modeled with significantly lower accuracy. Here, we show that incorporating differential reactivities from the NMIA and 1M6 reagents--which detect noncanonical and tertiary interactions--into prediction algorithms results in highly accurate secondary structure models for RNAs that were previously shown to be difficult to model. For these RNAs, 93% of accepted canonical base pairs were recovered in SHAPE-directed models. Discrepancies between accepted and modeled structures were small and appear to reflect genuine structural differences. Three-reagent SHAPE-directed modeling scales concisely to structurally complex RNAs to resolve the in-solution secondary structure analysis problem for many classes of RNA.
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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.