ArticleRNA (New York, N.Y.)2019
Estimating uncertainty in predicted folding free energy changes of RNA secondary structures.
Article in RNA (New York, N.Y.), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Structural and Thermodynamic Properties of RNA Molecules Using a Knowledge-Based Model.Journal of chemical theory and computation · 2026Article
- Hierarchical analysis of RNA secondary structures with pseudoknots based on sections.PLoS computational biology · 2026Article
- Structural Impact of 3-methylcytosine Modification on the Anticodon Stem-loop of a Neuronally-enriched Arginine tRNA.Journal of molecular biology · 2025Article
- Conformational dynamics of the hepatitis C virus 3'X RNA.RNA (New York, N.Y.) · 2024Article
- Estimating RNA Secondary Structure Folding Free Energy Changes with efn2.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects.Nucleic acids research · 2022Article
- Active secretion of a thermostable transglutaminase variant in Escherichia coli.Microbial cell factories · 2022Article
- Specific length and structure rather than high thermodynamic stability enable regulatory mRNA stem-loops to pause translation.Nature communications · 2022Article
- An in-silico approach to design potential siRNAs against the ORF57 of Kaposi's sarcoma-associated herpesvirus.Genomics & informatics · 2021Article
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Authors and funding
2 authors.
Funding
Abstract
Nearest neighbor parameters for estimating the folding stability of RNA are commonly used in secondary structure prediction, for generating folding ensembles of structures, and for analyzing RNA function. Previously, we demonstrated that we could quantify the uncertainties in each nearest neighbor parameter by perturbing the underlying optical melting data within experimental error and rederiving the parameters, which accounts for the substantial correlations that exist between the parameters. In this contribution, we describe a method to estimate uncertainty in the estimated folding stabilities of RNA structures, accounting for correlations in the nearest neighbor parameters. This method is incorporated in the RNA structure software package.
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