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PMID: 2479010 Published · ppublish English Journal Article Research Support, U.S. Gov't, P.H.S.

Improved predictions of secondary structures for RNA.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 86 ·No. 20 ·1989-10-00 ·Pages 7706-10

Jaeger JA, Turner DH, Zuker M

Abstract

The accuracy of computer predictions of RNA secondary structure from sequence data and free energy parameters has been increased to roughly 70%. Performance is judged by comparison with structures known from phylogenetic analysis. The algorithm also generates suboptimal structures. On average, the best structure within 10% of the lowest free energy contains roughly 90% of phylogenetically known helixes. The algorithm does not include tertiary interactions or pseudoknots and employs a crude model for single-stranded regions. The only favorable interactions are base pairing and stacking of terminal unpaired nucleotides at the ends of helixes. The excellent performance is consistent with these interactions being the primary interactions determining RNA secondary structure.

MeSH Terms
Base Composition Base Sequence Computer Simulation Models, Molecular Nucleic Acid Conformation RNA Software Thermodynamics
Chemicals
RNA
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Jaeger J A
Department of Chemistry, University of Rochester, NY 14627.
Turner D H
Zuker M
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Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.86.20.7706
Published
1989-10-00
Pages
7706-10
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC298139
Subset
IM
Grants
NIGMS NIH HHS · GM22939 · United States
External Links
PubMed source DOI: 10.1073/pnas.86.20.7706 PMC Full Text View journal details
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