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RNA. 2019 Jun;25(6):747-754. doi: 10.1261/rna.069203.118. Epub 2019 Apr 5.

Estimating uncertainty in predicted folding free energy changes of RNA secondary structures.

Author information

1
Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York, 14642, USA.
2
Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, New York, 14642, USA.

Abstract

Nearest neighbor parameters for estimating the folding stability of RNA are commonly used in secondary structure prediction, for generating folding ensembles of structures, and for analyzing RNA function. Previously, we demonstrated that we could quantify the uncertainties in each nearest neighbor parameter by perturbing the underlying optical melting data within experimental error and rederiving the parameters, which accounts for the substantial correlations that exist between the parameters. In this contribution, we describe a method to estimate uncertainty in the estimated folding stabilities of RNA structures, accounting for correlations in the nearest neighbor parameters. This method is incorporated in the RNA structure software package.

KEYWORDS:

Gibbs free energy change; nearest neighbor rules

PMID:
30952689
PMCID:
PMC6521603
[Available on 2020-06-01]
DOI:
10.1261/rna.069203.118
[Indexed for MEDLINE]

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