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

Ivan Dotu, Vinodh Mechery and Peter Clote

PLOS ONE, 2014, vol. 9, issue 2, 1-14

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/.

Date: 2014
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0085412

DOI: 10.1371/journal.pone.0085412

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