  Computational RNA secondary structure prediction is rather well established.
However, such prediction algorithms always depend on a large number of
experimentally measured parameters. Here, we study how sensitive structure
prediction algorithms are to changes in these parameters. We find that already
for changes corresponding to the actual experimental error to which these
parameters have been determined 30% of the structure are falsly predicted and
the ground state structure is preserved under parameter perturbation in only 5%
of all cases. We establish that base pairing probabilities calculated in a
thermal ensemble are a viable though not perfect measure for the reliability of
the prediction of individual structure elements. A new measure of stability
using parameter perturbation is proposed, and its limitations discussed.
