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Updated: May 2, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
Published on: December 9, 2022
Energy parameters and novel algorithms for an extended nearest neighbor energy model of RNA
Ivan Dotu1, Vinodh Mechery2, Peter Clote1
1Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America.
Abstract:
We describe the first algorithm and software, RNAenn, to compute the partition function and minimum free energy secondary structure for RNA with respect to an extended nearest neighbor energy model. Our next-nearest-neighbor triplet energy model appears to lead to somewhat more cooperative folding than does the nearest neighbor energy model, as judged by melting curves computed with RNAenn and with two popular software implementations for the nearest-neighbor energy model. A web server is available at http://bioinformatics.bc.edu/clotelab/RNAenn/.
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