Gesellschaft für Informatik e.V.

Lecture Notes in Informatics

German conference on bioinformatics 2010 P-173, 41-50 (2010).

Gesellschaft für Informatik, Bonn

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Shape-based barrier estimation for rnas

Sergiy Bogomolov , Martin Mann , Björn Voß , Andreas Podelski and Rolf Backofen


The ability of some RNA molecules to switch between different metastable conformations plays an important role in cellular processes. In order to identify such molecules and to predict their conformational changes one has to investigate the refolding pathways. As a qualitative measure of these transitions, the barrier height marks the energy peak along such refolding paths. We introduce a meta-heuristic to estimate such barriers, which is an NP-complete problem. To guide an arbitrary path heuristic, the method uses RNA shape representative structures as intermediate checkpoints for detours. This enables a broad but efficient search for refolding pathways. The resulting Shape Triples meta-heuristic enables a close to optimal estimation of the barrier height that outperforms the precision of the employed path heuristic.

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Gesellschaft für Informatik, Bonn
ISBN 978-3-88579-267-3

Last changed 04.10.2013 18:32:34