ArticleNucleic acids research2020
RNAProbe: a web server for normalization and analysis of RNA structure probing data.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Prediction of Ligand Binding to Transthyretin Using Machine Learning Algorithms and Low-Dimensional Molecular Descriptors: A Tox24 Challenge Study.Chemical research in toxicology · 2026Article
- Bridging sequence-structure motifs and genetic variants for genome-wide dynamic RNA-protein interaction profiling.Nature communications · 2026Article
- Exploring Secondary Structure Predictions for RNA-Targeted Drug Discovery: Power and Challenges.Journal of chemical information and modeling · 2026Article
- Enhanced Generalizability of RNA Secondary Structure Prediction via Convolutional Block Attention Network and Ensemble Learning.Molecules (Basel, Switzerland) · 2025Article
- Article
- IPANEMAP Suite: a pipeline for probing-informed RNA structure modeling.NAR genomics and bioinformatics · 2025Article
- RNA-Puzzles Round V: blind predictions of 23 RNA structures.Nature methods · 2025Article
- Transformers in RNA structure prediction: A review.Computational and structural biotechnology journal · 2025Review
- SimRNAweb v2.0: a web server for RNA folding simulations and 3D structure modeling, with optional restraints and enhanced analysis of folding trajectories.Nucleic acids research · 2024Article
- Conserved structures and dynamics in 5'-proximal regions of Betacoronavirus RNA genomes.Nucleic acids research · 2024Article
- Genome-Wide RNA Secondary Structure Prediction.Methods in molecular biology (Clifton, N.J.) · 2023Article
- RNA Chemical Labeling with Site-Specific, Relative Quantification by Mass Spectrometry for the Structural Study of a Neomycin-Sensing Riboswitch Aptamer Domain.ChemPlusChem · 2022Article
- Knotify: An Efficient Parallel Platform for RNA Pseudoknot Prediction Using Syntactic Pattern Recognition.Methods and protocols · 2022Article
- In Vitro Methods to Decipher the Structure of Viral RNA Genomes.Pharmaceuticals (Basel, Switzerland) · 2021Review
- Review
- Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements.Nucleic acids research · 2020Article
Corrections and comments
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Authors and funding
6 authors.
Funding
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Abstract
RNA molecules play key roles in all living cells. Knowledge of the structural characteristics of RNA molecules allows for a better understanding of the mechanisms of their action. RNA chemical probing allows us to study the susceptibility of nucleotides to chemical modification, and the information obtained can be used to guide secondary structure prediction. These experimental results can be analyzed using various computational tools, which, however, requires additional, tedious steps (e.g., further normalization of the reactivities and visualization of the results), for which there are no fully automated methods. Here, we introduce RNAProbe, a web server that facilitates normalization, analysis, and visualization of the low-pass SHAPE, DMS and CMCT probing results with the modification sites detected by capillary electrophoresis. RNAProbe automatically analyzes chemical probing output data and turns tedious manual work into a one-minute assignment. RNAProbe performs normalization based on a well-established protocol, utilizes recognized secondary structure prediction methods, and generates high-quality images with structure representations and reactivity heatmaps. It summarizes the results in the form of a spreadsheet, which can be used for comparative analyses between experiments. Results of predictions with normalized reactivities are also collected in text files, providing interoperability with bioinformatics workflows. RNAProbe is available at https://rnaprobe.genesilico.pl.
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