# Fast, approximate kinetics of RNA folding

Source: [Fast, approximate kinetics of RNA folding](<https://www.sota2.com/research/paper/68fa5ecb1e209131ce9e52e5>)

Collection index: [llms.txt](<https://www.sota2.com/research/llms.txt>)

Data updated: 2025-10-27T05:43:11.176Z

Authors: Evan Senter, Peter Clote

Published: 2015-01-19T21:24:34.000Z

## Abstract

In this paper, we introduce the software suite, Hermes, which provides fast, novel algorithms for RNA secondary structure kinetics. Using the fast Fourier transform to efficiently compute the Boltzmann probability that a secondary structure S of a given RNA sequence has base pair distance x \[resp. y\] from reference structure A \[resp. B\], Hermes computes the exact kinetics of folding from A to B in this coarse-grained model. In particular, Hermes computes the mean first passage time from the transition probability matrix by using matrix inversion, and also computes the equilibrium time from the rate matrix by using spectral decomposition. Due to the model granularity and the speed of Hermes, it is capable of determining secondary structure refolding kinetics for large RNA sequences, beyond the range of other methods. Comparative benchmarking of Hermes with other methods indicates that Hermes provides refolding kinetics of accuracy suitable for use in computational design of RNA, an important area of synthetic biology. Source code and documentation for Hermes are available at http://bioinformatics. bc.edu/clotelab/Hermes/.

## Recorded benchmark results

A research result applies to its stated dataset, split, metric and evaluation configuration. Compare like-for-like settings, preserve the metric's unit and direction, and distinguish paper-reported results from independent reproduction. The best result recorded here is not a claim of exhaustive, current global coverage.

## Original sources and implementation

[Original paper](<https://arxiv.org/abs/1501.04648>)

[PDF](<https://arxiv.org/pdf/1501.04648.pdf>)