Energy parameters and novel algorithms for an extended nearest neighbor energy model of RNA.
basic_science · Level V
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- Record sourced from PubMed, PMID 24586240.
- Also identified by DOI 10.1371/journal.pone.0085412 and PMC identifier 3931620.
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Abstract
We describe the first algorithm and software, RNAenn, to compute the partition function and minimum free energy secondary structure for RNA with respect to an extended nearest neighbor energy model. Our next-nearest-neighbor triplet energy model appears to lead to somewhat more cooperative folding than does the nearest neighbor energy model, as judged by melting curves computed with RNAenn and with two popular software implementations for the nearest-neighbor energy model. A web server is available at http://bioinformatics.bc.edu/clotelab/RNAenn/.
Medical subject headings
- Algorithms
- Energy Metabolism
- Models, Chemical
- Nucleic Acid Conformation
- RNA