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Posted by JPanek on 10 Aug 2011 at 12:24 GMT

However, the structure predicted might well be suboptimal for a number of reasons. These include inaccuracies of the energy model, kinetic folding effects, as well as neglecting tertiary structure.
http://ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002100#article1.body1.sec7.p4

Another reasons may exist, e.g. those already published in "The suboptimal structures find the optimal RNAs: homology search for bacterial non-coding RNAs using suboptimal RNA structures” by Pánek J, Krásny L, Bobek J, Jezková E, Korelusová J and Vohradsky J., Nucleic Acids Res. 2011 Apr;39(8):3418-26. Epub 2010 Dec 30.

No competing interests declared.