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A kinetic approach to the prediction of RNA secondary structures.

Research paper by A A AA Mironov, L P LP Dyakonova, A E AE Kister

Indexed on: 01 Feb '85Published on: 01 Feb '85Published in: Journal of biomolecular structure & dynamics



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.