An IP algorithm for RNA folding trajectories

DOI10.4230/LIPICS.WABI.2017.6MaRDI QIDQ5111796zbMATH OpenFDO

Authors Amir H. Bayegan, Peter Clote

Publication date 27 May 2020

Full work available at URL https://doi.org/10.4230/LIPICS.WABI.2017.6

zbMATH Keywords

conflict digraphfeedback vertex problemfolding trajectoryinteger programmingRNA secondary structure

Mathematics Subject Classification ID

Integer programming (90C10) Software, source code, etc. for problems pertaining to biology (92-04) Protein sequences, DNA sequences (92D20)

Recommendations

• scientific article; zbMATH DE number 4116366
• Speeding up the dynamic algorithm for planar RNA folding
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• RNA folding kinetics using Monte Carlo and Gillespie algorithms

Cites work

• Barrier heights between ground states in a model of RNA secondary structure
• Efficient computation of RNA folding dynamics
• Finding All the Elementary Circuits of a Directed Graph
• scientific article; zbMATH DE number 5542185 (Why is no real title available?)
• scientific article; zbMATH DE number 1062113 (Why is no real title available?)
• NP-completeness of the energy barrier problem without pseudoknots and temporary arcs
• Reducibility among combinatorial problems

Cited in

(7)

• A continuous analogue for RNA folding
• RNA folding kinetics using Monte Carlo and Gillespie algorithms
• RNA folding pathways and kinetics using 2D energy landscapes
• On finding all suboptimal foldings of an RNA molecule
• MS2distance
• scientific article; zbMATH DE number 6411942 (Why is no real title available?)
• DNA Computing

Describes a project that uses

Uses Software

• Tabu search
• ViennaRNA
• RNAsubopt
• KineFold

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