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A method for finding optimal rna secondary structures using a new entropy model (vsfold).

Wayne Dawson·Kazuya Fujiwara·Gota Kawai·Yasuhiro Futamura·Kenji Yamamoto
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Abstract

We are developing a program to calculate optimal RNA secondary structures. The model uses di-nucleotide pairing energies as with most traditional approaches. However, for long-range entropy interactions, the approach uses an entropy-loss model based on the accumulated sum of the entropy of bonding between each base-pair weighted inversely by the correlation of the RNA sequence (the Kuhn length). Stiff RNA forms very different structures from flexible RNA. The results demonstrate that the long-range folding is largely governed by this entropy and the Kuhn length.

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EntropyModels, ChemicalModels, MolecularMolecular StructureNucleic Acid ConformationRNAJournal ArticleResearch Support, Non-U.S. Gov't

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Wayne Dawson, Kazuya Fujiwara, Gota Kawai, Yasuhiro Futamura, Kenji Yamamoto. 2006. A method for finding optimal rna secondary structures using a new entropy model (vsfold).. https://doi.org/10.1080/15257770500446915

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