Authors

Y. Li;S. J. Zhang

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Abbreviated Journal Title

BMC Bioinformatics

Keywords

Q-BETA REPLICASE; SECONDARY STRUCTURE; BASE-STACKING; RIBOSWITCHES; STABILITY; MOLECULES; DYNAMICS; KINETICS; Biochemical Research Methods; Biotechnology & Applied Microbiology; Mathematical & Computational Biology

Abstract

Background: Accurately predicting low energy barrier folding pathways between conformational secondary structures of an RNA molecule can provide valuable information for understanding its catalytic and regulatory functions. Most existing heuristic algorithms guide the construction of folding pathways by free energies of intermediate structures in the next move during the folding. However due to the size and ruggedness of RNA energy landscape, energy-guided search can become trapped in local optima. Results: In this paper, we propose an algorithm that guides the construction of folding pathways through the formation and destruction of RNA stacks. Guiding the construction of folding pathways by coarse grained movements of RNA stacks can help reduce the search space and make it easier to jump out of local optima. RNAEAPath is able to find lower energy barrier folding pathways between secondary structures of conformational switches and outperforms the existing heuristic algorithms in most test cases. Conclusions: RNAEAPath provides an alternate approach for predicting low-barrier folding pathways between RNA conformational secondary structures. The source code of RNAEAPath and the test data sets are available at http://genome.ucf.edu/RNAEAPath.

Journal Title

Bmc Bioinformatics

Volume

13

Publication Date

1-1-2012

Document Type

Article; Proceedings Paper

Language

English

First Page

13

WOS Identifier

WOS:000303936300005

ISSN

1471-2105

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