Energy Parameters and Novel Algorithms for an Extended Nearest Neighbor Energy Model of RNA

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 t...

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Detalles Bibliográficos
Autores principales: Dotu, Ivan, Mechery, Vinodh, Clote, Peter
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2014
Materias:
Research Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3931620/
https://www.ncbi.nlm.nih.gov/pubmed/24586240
http://dx.doi.org/10.1371/journal.pone.0085412
Descripción
Sumario: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/.

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