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
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author Dotu, Ivan
Mechery, Vinodh
Clote, Peter
author_facet Dotu, Ivan
Mechery, Vinodh
Clote, Peter
author_sort Dotu, Ivan
collection PubMed
description 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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spelling pubmed-39316202014-02-25 Energy Parameters and Novel Algorithms for an Extended Nearest Neighbor Energy Model of RNA Dotu, Ivan Mechery, Vinodh Clote, Peter PLoS One Research Article 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/. Public Library of Science 2014-02-21 /pmc/articles/PMC3931620/ /pubmed/24586240 http://dx.doi.org/10.1371/journal.pone.0085412 Text en © 2014 Dotu et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Dotu, Ivan
Mechery, Vinodh
Clote, Peter
Energy Parameters and Novel Algorithms for an Extended Nearest Neighbor Energy Model of RNA
title Energy Parameters and Novel Algorithms for an Extended Nearest Neighbor Energy Model of RNA
title_full Energy Parameters and Novel Algorithms for an Extended Nearest Neighbor Energy Model of RNA
title_fullStr Energy Parameters and Novel Algorithms for an Extended Nearest Neighbor Energy Model of RNA
title_full_unstemmed Energy Parameters and Novel Algorithms for an Extended Nearest Neighbor Energy Model of RNA
title_short Energy Parameters and Novel Algorithms for an Extended Nearest Neighbor Energy Model of RNA
title_sort energy parameters and novel algorithms for an extended nearest neighbor energy model of rna
topic Research Article
url 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
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