Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization.

By D. Mathews. RNA: A publication of the RNA Society, 2004

387 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/8277ea73ecd7100cff0f17d23fbdb419c98933fa

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Citations in the corpus

RNAplex: a fast tool for RNA-RNA interaction search (2008, background): “They are based upon a large number of measurements performed on small RNAs and the assumption that stacking base pairs and loop entropies contribute, additively to the free energy of RNA secondary structures ( Mathews, 2004; Mathews et al., 1999).”
Thermodynamic Analysis of Interacting Nucleic Acid Strands (2007, methodology): “These tools are useful in practice for the analysis and design of functional nucleic acid systems [8, 22, 12, 29, 28].”
Pervasive tertiary structure in the dengue virus RNA genome (2018, methodology): “6) and both 1M7 and differential SHAPE reactivities (using 1M6 and NMIA data) (6) was used to calculate a global partition function (10, 11), which yields base-pairing probabilities for all possible canonical base pairs.”
A benchmark of multiple sequence alignment programs upon structural RNAs (2005, background): “A second structural RNA alignment approach employs (predicted) structures and aligns these directly [19–21], again these are generally limited in terms of sequence size, but primarily suffer from the inaccuracy of single sequence structure prediction [22–24] (although, pruning low probability base-p”
A comprehensive comparison of comparative RNA structure prediction approaches (2004, background): “Selectivity is also known as the "specificity" [28] and "positive predictive value" [64,65].”
RNAstructure: software for RNA secondary structure prediction and analysis (2010, methodology): “For example, base pair probabilities can be determined using a partition function and highly probable pairs are more likely to be correctly predicted pairs [22].”