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. 1982 Jan 11;10(1):403–419. doi: 10.1093/nar/10.1.403

Computer-aided prediction of RNA secondary structures.

P E Auron, W P Rindone, C P Vary, J J Celentano, J N Vournakis
PMCID: PMC326142  PMID: 6174937

Abstract

A brief survey of computer algorithms that have been developed to generate predictions of the secondary structures of RNA molecules is presented. Two particular methods are described in some detail. The first utilizes a thermodynamic energy minimization algorithm that takes into account the likelihood that short-range folding tends to be favored over long-range interactions. The second utilizes an interactive computer graphic modelling algorithm that enables the user to consider thermodynamic criteria as well as structural data obtained by nuclease susceptibility, chemical reactivity and phylogenetic studies. Examples of structures for prokaryotic 16S and 23S ribosomal RNAs, several eukaryotic 5S ribosomal RNAs and rabbit beta-globin messenger RNA are presented as case studies in order to describe the two techniques. Anm argument is made for integrating the two approaches presented in this paper, enabling the user to generate proposed structures using thermodynamic criteria, allowing interactive refinement of these structures through the application of experimentally derived data.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

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