RNA folding kinetics using Monte Carlo and Gillespie algorithms

DOI10.1007/s00285-017-1169-7zbMath1392.92066arXiv1707.03922OpenAlexW2963996765WikidataQ47737296 ScholiaQ47737296MaRDI QIDQ1741906

Peter Clote, Amir H. Bayegan

Publication date: 10 April 2018

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

Full work available at URL: https://arxiv.org/abs/1707.03922

zbMATH Keywords

Metropolis algorithmGillespie algorithmRNA secondary structuremean first passage timemean recurrence timeexpected network degreerefolding kinetics

Mathematics Subject Classification ID

Computational methods in Markov chains (60J22) Monte Carlo methods (65C05) Other programming paradigms (object-oriented, sequential, concurrent, automatic, etc.) (68N19) Protein sequences, DNA sequences (92D20)

Related Items (1)

RNAexpNumNbors

Uses Software

• Rfam
• ViennaRNA
• FFTbor2D
• KFOLD
• ERD
• MSMBuilder
• FFTbor
• MODENA
• NNDB

Cites Work

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• RNA secondary structures and their prediction
• Funnels in energy landscapes
• On some new sequences generalizing the Catalan and Motzkin numbers
• Combinatorics of locally optimal RNA secondary structures
• RNA folding pathways and kinetics using 2D energy landscapes
• The Role of the Group Generalized Inverse in the Theory of Finite Markov Chains
• Efficient computation of RNA folding dynamics
• Equation of State Calculations by Fast Computing Machines
• Monte Carlo sampling methods using Markov chains and their applications

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