RNA folding pathways and kinetics using 2D energy landscapes

DOI10.1007/S00285-014-0760-4zbMath1308.92079OpenAlexW2038166314WikidataQ51113118 ScholiaQ51113118MaRDI QIDQ2512926

Evan Senter, Peter Clote, Ivan Dotu

Publication date: 2 February 2015

Published in: Journal of Mathematical Biology (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1007/s00285-014-0760-4

zbMATH Keywords

dynamic programmingFFTkineticspolynomial interpolationRNABoltzman partition function

Mathematics Subject Classification ID

Computational methods in Markov chains (60J22) Other programming paradigms (object-oriented, sequential, concurrent, automatic, etc.) (68N19) Protein sequences, DNA sequences (92D20) Molecular physics (81V55) Compliance or weight optimization in solid mechanics (74P05)

Related Items (1)

RNA folding kinetics using Monte Carlo and Gillespie algorithms

Uses Software

• Unnamed Item
• FFTW
• RNA2Dfold
• FFTbor2D
• KineFold

Cites Work

• Unnamed Item
• LAPACK Users' Guide
• The Role of the Group Generalized Inverse in the Theory of Finite Markov Chains
• Barrier heights between ground states in a model of RNA secondary structure
• Efficient computation of RNA folding dynamics

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