ArticleBioinformatics (Oxford, England)2016
AccessFold: predicting RNA-RNA interactions with consideration for competing self-structure.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Benchmarking the methods for predicting base pairs in RNA-RNA interactions.Bioinformatics (Oxford, England) · 2025Article
- Experimental and computational methods for studying the dynamics of RNA-RNA interactions in SARS-COV2 genomes.Briefings in functional genomics · 2024Review
- 3D feasibility of 2D RNA-RNA interaction paths by stepwise folding simulations.RNA (New York, N.Y.) · 2024Article
- How to do RNA-RNA Interaction Prediction? A Use-Case Driven Handbook Using IntaRNA.Methods in molecular biology (Clifton, N.J.) · 2024Review
- A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools.Briefings in bioinformatics · 2023Review
- LinearCoFold and LinearCoPartition: linear-time algorithms for secondary structure prediction of interacting RNA molecules.Nucleic acids research · 2023Article
- RNA Secondary Structure Analysis Using RNAstructure.Current protocols · 2023Article
- Potential of siRNA in COVID-19 therapy: Emphasis onFrontiers in bioengineering and biotechnology · 2023Review
- The Four mRNA Bases Have Quite Different (Un)folding Free Energies, Applications to RNA Splicing and Translation Initiation with BindOligoNet.Journal of molecular biology · 2022Article
- Signaling pathways of genetic variants and miRNAs in the pathogenesis of myasthenia gravis.Gland surgery · 2020Article
- LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities.Bioinformatics (Oxford, England) · 2020Article
- The impact of various seed, accessibility and interaction constraints on sRNA target prediction- a systematic assessment.BMC bioinformatics · 2020Article
- High-throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites.Nature communications · 2018Article
- Optimization of a novel biophysical model using large scale in vivo antisense hybridization data displays improved prediction capabilities of structurally accessible RNA regions.Nucleic acids research · 2017Article
- A comprehensive benchmark of RNA-RNA interaction prediction tools for all domains of life.Bioinformatics (Oxford, England) · 2017Article
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Authors and funding
3 authors.
Funding
Abstract
motivationThere are numerous examples of RNA-RNA complexes, including microRNA-mRNA and small RNA-mRNA duplexes for regulation of translation, guide RNA interactions with target RNA for post-transcriptional modification and small nuclear RNA duplexes for splicing. Predicting the base pairs formed between two interacting sequences remains difficult, at least in part because of the competition between unimolecular and bimolecular structure.
resultsTwo algorithms were developed for improved prediction of bimolecular RNA structure that consider the competition between self-structure and bimolecular structure. These algorithms utilize two novel approaches to evaluate accessibility: free energy density minimization and pseudo-energy minimization. Free energy density minimization minimizes the folding free energy change per nucleotide involved in an intermolecular secondary structure. Pseudo-energy minimization (called AccessFold) minimizes the sum of free energy change and a pseudo-free energy penalty for bimolecular pairing of nucleotides that are unlikely to be accessible for bimolecular structure. The pseudo-free energy, derived from unimolecular pairing probabilities, is applied per nucleotide in bimolecular pairs, and this approach is able to predict binding sites that are split by unimolecular structures. A benchmark set of 17 bimolecular RNA structures was assembled to assess structure prediction. Pseudo-energy minimization provides a statistically significant improvement in sensitivity over the method that was found in a benchmark to be the most accurate previously available method, with an improvement from 36.8% to 57.8% in mean sensitivity for base pair prediction. AVAILABILITY AND IMPLEMENTATION: Pseudo-energy minimization is available for download as AccessFold, under an open-source license and as part of the RNAstructure package, at: http://rna.urmc.rochester.edu/RNAstructure.html CONTACT: david_mathews@urmc.rochester.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.