ArticleNucleic acids research2020
IPANEMAP: integrative probing analysis of nucleic acids empowered by multiple accessibility profiles.
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 10 papers.
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Who cites it
10 citing papers in PubMed, 19 citations in OpenAlex.
- MERGE-RNA: a physics-based model to predict RNA secondary structure ensembles with chemical probing.Nucleic acids research · 2026Article
- Designing molecular RNA switches with Restricted Boltzmann machines.Nature communications · 2025Article
- DEAD-box helicase intrinsically disordered domains and structural dynamics of HIV-1 RNA are required to reveal DDX3X catalytic efficiency.Nucleic acids research · 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
- A Guide to Computational Cotranscriptional Folding Featuring the SRP RNA.Methods in molecular biology (Clifton, N.J.) · 2024Article
- RNA Secondary Structure Modeling Following the IPANEMAP Workflow.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
- sRNA-controlled iron sparing response in Staphylococci.Nucleic acids research · 2022Article
- Progress toward SHAPE Constrained Computational Prediction of Tertiary Interactions in RNA Structure.Non-coding RNA · 2021Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The manual production of reliable RNA structure models from chemical probing experiments benefits from the integration of information derived from multiple protocols and reagents. However, the interpretation of multiple probing profiles remains a complex task, hindering the quality and reproducibility of modeling efforts. We introduce IPANEMAP, the first automated method for the modeling of RNA structure from multiple probing reactivity profiles. Input profiles can result from experiments based on diverse protocols, reagents, or collection of variants, and are jointly analyzed to predict the dominant conformations of an RNA. IPANEMAP combines sampling, clustering and multi-optimization, to produce secondary structure models that are both stable and well-supported by experimental evidences. The analysis of multiple reactivity profiles, both publicly available and produced in our study, demonstrates the good performances of IPANEMAP, even in a mono probing setting. It confirms the potential of integrating multiple sources of probing data, informing the design of informative probing assays.
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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 Socratic graph.