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PMID: 7684834 Published · ppublish English Journal Article

Prediction of alternative RNA secondary structures based on fluctuating thermodynamic parameters.

Nucleic acids research ·Vol. 21 ·No. 9 ·1993-05-11 ·Pages 2173-8

Le SY, Chen JH, Maizel JV

Abstract

In this paper we present a new method for predicting a set of RNA secondary structures that are thermodynamically favored in RNA folding simulations. This method uses a large number of 'simulated energy rules' (SER) generated by perturbing the free energy parameters derived experimentally within the range of the experimental errors. The structure with the lowest free energy is computed for each SER. Structural comparisons are used to avoid multiple generation of similar structures. Computed structures are evaluated using the energy distribution of the lowest free energy structures derived in the simulation. Predicted be graphically displayed with their occurring frequencies in the simulation by dot-plot representations. On average, about 90% of phylogenetic helixes in the known models of tRNA, Group I self-splicing intron, and Escherichia coli 16 S rRNA, were predicted using the method.

MeSH Terms
Algorithms Animals Bombyx/genetics Computer Simulation Escherichia coli/genetics Nucleic Acid Conformation RNA/chemistry RNA, Bacterial/chemistry RNA, Protozoan/chemistry Tetrahymena thermophila/genetics Thermodynamics
Chemicals
RNA, Bacterial RNA, Protozoan RNA
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Le S Y
Laboratory of Mathematical Biology, National Cancer Institute, NIH, Frederick, MD 21702.
Chen J H
Maizel J V
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/21.9.2173
Published
1993-05-11
Pages
2173-8
Language
English
Region
England
NLM ID
0411011
PMCID
PMC309481
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/21.9.2173 PMC Full Text View journal details
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