A partition function algorithm for nucleic acid secondary structure including pseudoknots

By Robert M. Dirks, Niles A. Pierce. Journal of Computational Chemistry, 2003

399 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/2e638f60ddeba56737dca529e52e1292d3714956

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Citations in the corpus

IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming (2011, methodology): “Examples of exact methods are DP algorithms that predict limited classes of pseudoknots in O(n4)∼O(n6) time (Akutsu, 2000; Dirks and Pierce, 2003; Lyngsø and Pedersen, 2000a; Reeder and Giegerich, 2004; Rivas and Eddy, 1999), where n is the length of an input RNA sequence.”
Using Rosetta for RNA homology modeling (2019, methodology): “If an Rfam family or extensive sequence alignment is not available, tools for secondary structure prediction including RNAstructure (Reuter & Mathews, 2010), NUPACK (Dirks & Pierce, 2003), ViennaRNA (Lorenz et al., 2011), and CONTRAfold (Do, Woods, & Batzoglou, 2006) are appropriate although none re”
A comprehensive comparison of comparative RNA structure prediction approaches (2004, methodology): “An implementation of the single sequence pseudoknot algorithms [42,43,94] employing similar strategies to RNAalifold [21] for alignment folding would be most useful.”
Thermodynamic Analysis of Interacting Nucleic Acid Strands (2007, methodology): “2See [10] for an extended description of the algorithm, including details on how to reduce the time complexity to O(N3) [21] by exploiting certain intricacies of the loop-based free energy model.”
Thermodynamics of RNA-RNA Binding (2006, background): “These cases could in principle be handled using a generic approach to pseudo-knotted RNA structures [7, 8] at the expense of much more costly computations.”