ArticleBioinformatics (Oxford, England)2012
An RNA Mapping DataBase for curating RNA structure mapping experiments.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed.
- UFold-X: an enhanced Dual & Dynamic U-Mamba model for long-range RNA secondary structure prediction.Nucleic acids research · 2026Article
- Co-transcriptional folding orchestrates sequential multi-effector sensing by a glycine tandem riboswitch.Nature communications · 2026Article
- Enhanced RNA secondary structure prediction through integrative deep learning and structural context analysis.Nucleic acids research · 2025Article
- Sequential structure probing of cotranscriptional RNA folding intermediates.Nature communications · 2025Article
- Article
- How Parameters Influence SHAPE-Directed Predictions.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Observation of coordinated RNA folding events by systematic cotranscriptional RNA structure probing.Nature communications · 2023Article
- Molecular Dynamics Simulations with Grand-Canonical Reweighting Suggest Cooperativity Effects in RNA Structure Probing Experiments.Journal of chemical theory and computation · 2023Article
- RNA independent fragment partition method based on deep learning for RNA secondary structure prediction.Scientific reports · 2023Article
- Shapify: Paths to SARS-CoV-2 frameshifting pseudoknot.PLoS computational biology · 2023Article
- Non-coding RNAs in human health and disease: potential function as biomarkers and therapeutic targets.Functional & integrative genomics · 2023Review
- RNA secondary structure packages evaluated and improved by high-throughput experiments.Nature methods · 2022Article
- Programmable antivirals targeting critical conserved viral RNA secondary structures from influenza A virus and SARS-CoV-2.Nature medicine · 2022Article
- Short- and long-range interactions in the HIV-1 5' UTR regulate genome dimerization and packaging.Nature structural & molecular biology · 2022Article
- Characteristic chemical probing patterns of loop motifs improve prediction accuracy of RNA secondary structures.Nucleic acids research · 2021Article
- Sieving RNA 3D Structures with SHAPE and Evaluating Mechanisms Driving Sequence-Dependent Reactivity Bias.The journal of physical chemistry. B · 2021Article
- RASP: an atlas of transcriptome-wide RNA secondary structure probing data.Nucleic acids research · 2021Article
- The lncRNA Toolkit: Databases and In Silico Tools for lncRNA Analysis.Non-coding RNA · 2020Review
- Folding heterogeneity in the essential human telomerase RNA three-way junction.RNA (New York, N.Y.) · 2020Article
- Machine learning a model for RNA structure prediction.NAR genomics and bioinformatics · 2020Article
Corrections and comments
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3 authors.
Funding
Abstract
summaryWe have established an RNA mapping database (RMDB) to enable structural, thermodynamic and kinetic comparisons across single-nucleotide-resolution RNA structure mapping experiments. The volume of structure mapping data has greatly increased since the development of high-throughput sequencing techniques, accelerated software pipelines and large-scale mutagenesis. For scientists wishing to infer relationships between RNA sequence/structure and these mapping data, there is a need for a database that is curated, tagged with error estimates and interfaced with tools for sharing, visualization, search and meta-analysis. Through its on-line front-end, the RMDB allows users to explore single-nucleotide-resolution mapping data in heat-map, bar-graph and colored secondary structure graphics; to leverage these data to generate secondary structure hypotheses; and to download the data in standardized and computer-friendly files, including the RDAT and community-consensus SNRNASM formats. At the time of writing, the database houses 53 entries, describing more than 2848 experiments of 1098 RNA constructs in several solution conditions and is growing rapidly. AVAILABILITY: Freely available on the web at http://rmdb.stanford.edu. CONTACT: rhiju@stanford.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Online.
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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.