Publications - Published papers

Please find below publications of our group. Currently, we list 496 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (access) is restricted to our local network and chosen collaborators. If you have problems accessing electronic information, please let us know:

©NOTICE: All papers are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.

Thermodynamics of RNA-RNA Binding

Ulrike Mückstein, Hakim Tafer, Jörg Hackermüller, Stephan Bernhard, Peter F. Stadler, Ivo L. Hofacker


PREPRINT 05-019: [ PDF ]  [ PS ]
[ Publishers's page ]  paperID


Bioinformatics 22: 1177-1182 (2006)


We present an extension of the standard partition function approach to RNA secondary structures that computes the probabilities Pu[i; j] that a sequence interval [i;j] is unpaired. Comparison with experimental data shows that Pu[i; j] can be applied as a signicant determinant of local target site accessibility for RNA interference (RNAi). Furthermore these quantities can be used to rigorously determine binding free energies of short oligomers to large mRNA targets. The resource consumption is comparable to a single partition function computation for the large target molecule. We can show that RNAi eciency correlates well with the binding probabilities of the siRNAs to their respective mRNA target.


RNA secondary structure, RNA hybridization, dynamic programming


Earlier version in: German Conference on Bioinformatics 2005, pp. 3-13; A. Torda, S. Kurtz, M. Rarey (eds.), LNI P-71 Gesellschaft f. Informatik, Bonn, 2005.