ArticleAlgorithms for molecular biology : AMB2006
Partition function and base pairing probabilities of RNA heterodimers.
Article in Algorithms for molecular biology : AMB, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 140 papers.
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140 citing papers in PubMed.
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- Exploitation of Biocomputational Approaches for siRNA-Mediated Gene Silencing of HPV: A Novel Therapeutic Strategy for Cervical Cancer.Cancer reports (Hoboken, N.J.) · 2025Article
- Propagation of [D1,2]-type spliceosomal twin introns (stwintrons) inMicrobiology spectrum · 2025Article
- Modeling RNA duplex dynamics with Gibbs sampling enhances base-pair prediction accuracy and reveals structural activity profiles.NAR genomics and bioinformatics · 2025Article
- Comprehensive analysis of Saccharomyces cerevisiae intron structures in vivo.Nature structural & molecular biology · 2025Article
- RegRNA 3.0: expanding regulatory RNA analysis with new features for motif, interaction, and annotation.Nucleic acids research · 2025Article
- Benchmarking the methods for predicting base pairs in RNA-RNA interactions.Bioinformatics (Oxford, England) · 2025Article
- Tuning Ultrasensitivity in Genetic Logic Gates Using Antisense RNA Feedback.ACS synthetic biology · 2025Article
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- Mammalian piRNA target prediction using a hierarchical attention model.BMC bioinformatics · 2025Article
- RNA encodes physical information.bioRxiv : the preprint server for biology · 2024Article
- Genome-Wide Dissection of Selection on microRNA Target Genes Involved in Rice Flower Development.Plants (Basel, Switzerland) · 2024Article
- 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
80 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRNA has been recognized as a key player in cellular regulation in recent years. In many cases, non-coding RNAs exert their function by binding to other nucleic acids, as in the case of microRNAs and snoRNAs. The specificity of these interactions derives from the stability of inter-molecular base pairing. The accurate computational treatment of RNA-RNA binding therefore lies at the heart of target prediction algorithms.
methodsThe standard dynamic programming algorithms for computing secondary structures of linear single-stranded RNA molecules are extended to the co-folding of two interacting RNAs.
resultsWe present a program, RNAcofold, that computes the hybridization energy and base pairing pattern of a pair of interacting RNA molecules. In contrast to earlier approaches, complex internal structures in both RNAs are fully taken into account. RNAcofold supports the calculation of the minimum energy structure and of a complete set of suboptimal structures in an energy band above the ground state. Furthermore, it provides an extension of McCaskill's partition function algorithm to compute base pairing probabilities, realistic interaction energies, and equilibrium concentrations of duplex structures.
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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.