Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots

By Tatsuya Akutsu. Discrete Applied Mathematics, 2000

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Thermodynamic Analysis of Interacting Nucleic Acid Strands (2007, background): “specification of polynomial-time MFE determination [30, 1] and partition function [10, 11] algorithms.”
Knowledge-based machine learning methods for macromolecular 3D structure prediction (2016, background): “The base pairing states can be predicted using some secondary structure prediction programs (Akutsu, 2000; Do et al., 2006; Eddy and Durbin, 1994; Gardner and Giegerich, 2004; Knudsen and Hein, 2003; Mathews and Turner, 2006; Poolsap et al., 2009; Zuker, 2003) with reasonable accuracy.”
RNAplex: a fast tool for RNA-RNA interaction search (2008, background): “Availability: RNAplex can be downloaded at http://www.tbi.univie. ac.at/ htafer/ Contact: ivo@tbi.univie.ac.at Supplementary information: Supplementary data are available at Bioinformatics online.”
IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming (2011, background): “This is a drawback of our method.”