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

zbMATH Keywords

integer programmingRNA secondary structureconflict digraphfeedback vertex problemfolding trajectory

Mathematics Subject Classification ID

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

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Cites work

• scientific article; zbMATH DE number 5542185 (Why is no real title available?)
• scientific article; zbMATH DE number 1062113 (Why is no real title available?)
• 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
• NP-completeness of the energy barrier problem without pseudoknots and temporary arcs
• Reducibility among combinatorial problems

Cited in

(7)

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

Describes a project that uses

Uses Software

• Tabu search
• ViennaRNA
• RNAsubopt
• KineFold

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