ArticleMethods in molecular biology (Clifton, N.J.)2024
Estimating RNA Secondary Structure Folding Free Energy Changes with efn2.
Article in Methods in molecular biology (Clifton, N.J.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed.
- A crucial role for novel miR-12137-3p in supporting weight gain in treatment naïve HIV-infected patients on antiretroviral therapies.Journal of translational medicine · 2026Trial
- An efficient algorithm for exploring RNA branching conformations under the nearest-neighbor thermodynamic model.Algorithms for molecular biology : AMB · 2026Article
- Can geometric combinatorics improve RNA branching predictions?BMC bioinformatics · 2025Article
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2 authors.
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Abstract
A number of analyses require estimates of the folding free energy changes of specific RNA secondary structures. These predictions are often based on a set of nearest neighbor parameters that models the folding stability of a RNA secondary structure as the sum of folding stabilities of the structural elements that comprise the secondary structure. In the software suite RNAstructure, the free energy change calculation is implemented in the program efn2. The efn2 program estimates the folding free energy change and the experimental uncertainty in the folding free energy change. It can be run through the graphical user interface for RNAstructure, from the command line, or a web server. This chapter provides detailed protocols for using efn2.
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