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Using complex roots of unity and the Fast Fourier Transform, we design a new thermodynamics-based algorithm, FFTbor, that computes the Boltzmann probability that secondary structures differ by [Formula: see text] base pairs from an arbitrary initial structure of a given RNA sequence. The algorithm, which runs in quartic time O(n(4)) and quadratic space(More)
Transmembrane β-barrel (TMB) proteins are a special class of transmembrane proteins which play several key roles in human body and diseases. Due to experimental difficulties, the number of TMB proteins with known structures is very small. Over the years, a number of learning-based methods have been introduced for recognition and structure prediction(More)
Transmembrane β-barrel proteins are a special class of transmembrane proteins which play several key roles in human body and diseases. Due to experimental difficulties, the number of transmembrane β-barrel proteins with known structures is very small. Over the years, a number of learning-based methods have been introduced for recognition and structure(More)
Using the Fast Fourier Transform to accelerate the computational search for RNA conformational switches Evan Senter, Saad Sheikh, Ivan Dotu, Yann Ponty, and Peter Clote 1 Biology Department, Boston College, Chestnut Hill MA 02467 USA clote@bc.edu,ivan.dotu@bc.edu,evansenter@gmail.com 2 Computer Science Department, University of Florida, Gainesville FL 32601(More)
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