@inproceedings{dd328c46e6cc41c19d99c8cb6ca777ba,
title = "Abstract: Using the fast Fourier transform to accelerate the computational search for RNA conformational switches",
abstract = "We describe the broad outline of a new thermodynamics-based algorithm, FFTbor, that uses the fast Fourier transform to perform polynomial interpolation to compute the Boltzmann probability that secondary structures differ by k base pairs from an arbitrary reference structure of a given RNA sequence. The algorithm, which runs in quartic time O(n4) and quadratic space O(n2), is used to determine the correlation between kinetic folding speed and the ruggedness of the energy landscape, and to predict the location of riboswitch expression platform candidates. The full paper appears in PLoS ONE (2012) 19 Dec 2012. A web server is available at http://bioinformatics.bc.edu/ clotelab/FFTbor/.",
keywords = "Lagrange interpolation, RNA secondary structure, fast Fourier transform, partition function",
author = "Evan Senter and Saad Sheikh and Ivan Dotu and Yann Ponty and Peter Clote",
year = "2013",
month = apr,
day = "3",
doi = "10.1007/978-3-642-37195-0\_22",
language = "English",
isbn = "9783642371943",
series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",
pages = "264--265",
booktitle = "Research in Computational Molecular Biology - 17th Annual International Conference, RECOMB 2013, Proceedings",
note = "17th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2013 ; Conference date: 07-04-2013 Through 10-04-2013",
}