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  4. BarMap: RNA folding on dynamic energy landscapes
 
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2010
Journal Article
Title

BarMap: RNA folding on dynamic energy landscapes

Abstract
Dynamical changes of RNA secondary structures play an important role in the function of many regulatory RNAs. Such kinetic effects, especially in time-variable and externally triggered systems, are usually investigated by means of extensive and expensive simulations of large sets of individual folding trajectories. Here we describe the theoretical foundations of a generic approach that not only allows the direct computation of approximate population densities but also reduces the efforts required to analyze the folding energy landscapes to a one-time preprocessing step. The basic idea is to consider the kinetics on individual landscapes and to model external triggers and environmental changes as small but discrete changes in the landscapes. A "barmap" links macrostates of temporally adjacent landscapes and defines the transfer of population densities from one "snapshot" to the next. Implemented in the BarMap software, this approach makes it feasible to study folding processes at the level of basins, saddle points, and barriers for many nonstationary scenarios, including temperature changes, cotranscriptional folding, refolding in consequence to degradation, and mechanically constrained kinetics, as in the case of the translocation of a polymer through a pore.
Author(s)
Hofacker, Ivo L.
Universität Wien
Flamm, Christoph
Universität Wien
Heine, Christian
incore IT Solutions OG Wien
Wolfinger, Michael T.
Universität Wien
Scheuermann, Gerik
Universität Leipzig
Stadler, Peter F.
Fraunhofer-Institut für Zelltherapie und Immunologie IZI  
Journal
RNA  
Open Access
DOI
10.1261/rna.2093310
Additional full text version
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Language
English
Fraunhofer-Institut für Zelltherapie und Immunologie IZI  
Keyword(s)
  • RNA folding kinectics

  • barrier tree

  • dynamic energy landscape

  • cotranscriptional folding

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