An IP algorithm for RNA folding trajectories

DOI10.4230/LIPICS.WABI.2017.6zbMATH Open1443.92135MaRDI QIDQ5111796FDOQ5111796

Authors: Amir H. Bayegan, Peter Clote 

Publication date: 27 May 2020

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• Speeding up the dynamic algorithm for planar RNA folding
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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)

Cites Work

• Title not available (Why is that?)
• Reducibility among combinatorial problems
• Title not available (Why is that?)
• Finding All the Elementary Circuits of a Directed Graph
• Barrier heights between ground states in a model of RNA secondary structure
• Efficient computation of RNA folding dynamics
• NP-completeness of the energy barrier problem without pseudoknots and temporary arcs

Cited In (7)

• A continuous analogue for RNA folding
• RNA folding pathways and kinetics using 2D energy landscapes
• MS2distance
• Title not available (Why is that?)
• On finding all suboptimal foldings of an RNA molecule
• DNA Computing
• RNA folding kinetics using Monte Carlo and Gillespie algorithms

Uses Software

• Tabu search
• ViennaRNA
• RNAsubopt
• KineFold

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