Improved predictions of secondary structures for RNA.

Jaeger JA; Turner DH; Zuker M

Department of Chemistry, University of Rochester, NY 14627.

Proc Natl Acad Sci U S A 86: 7706-10 (1989)

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 Headings

Base Composition

Base Sequence

Computer Simulation*

Models, Molecular*

Nucleic Acid Conformation*

RNA*

Software

Support, U.S. Gov't, P.H.S.

Thermodynamics

Unique Identifier: 90046664