Estimating uncertainty in predicted folding free energy changes of RNA secondary structures.
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.
['Zuber|Jeffrey|J|', 'Mathews|David H|DH|']
D000465:Algorithms D020029:Base Pairing D001483:Base Sequence D006801:Humans D012313:RNA D059370:RNA Folding D012984:Software D013816:Thermodynamics D035501:Uncertainty
Gibbs free energy change nearest neighbor rules