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Simulation of Folding Kinetics for Aligned RNAs.

Jiabin HuangBjörn Voß
Published in: Genes (2021)
Studying the folding kinetics of an RNA can provide insight into its function and is thus a valuable method for RNA analyses. Computational approaches to the simulation of folding kinetics suffer from the exponentially large folding space that needs to be evaluated. Here, we present a new approach that combines structure abstraction with evolutionary conservation to restrict the analysis to common parts of folding spaces of related RNAs. The resulting algorithm can recapitulate the folding kinetics known for single RNAs and is able to analyse even long RNAs in reasonable time. Our program RNAliHiKinetics is the first algorithm for the simulation of consensus folding kinetics and addresses a long-standing problem in a new and unique way.
Keyphrases
  • machine learning
  • single molecule
  • molecular dynamics simulations
  • deep learning
  • virtual reality
  • genome wide
  • clinical practice