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A kinetic approach to the prediction of RNA secondary structures.

Authors
Type
Published Article
Journal
Journal of biomolecular structure & dynamics
Publication Date
Volume
2
Issue
5
Pages
953–962
Identifiers
PMID: 2477031
Source
Medline

Abstract

A new approach to the prediction of secondary RNA structures based on the analysis of the kinetics of molecular self-organisation is proposed herein. The Markov process is used to describe structural reconstructions during secondary structure formation. This process is modelled by a Monte-Carlo method. Examples of the calculation by this method of the secondary structures kinetic ensemble are given. Distribution of time-dependent probabilities within the ensembles is obtained. An effective method for search for the equilibrium ensemble is also suggested. This method is based on the construction of a tree of all possible secondary structures of RNA. By ascribing a probability for each structure (according to its free energy) the Boltzmann equilibrium ensemble can be obtained.

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