How to determine whether a secondary structure prediction is significant or relevant?

Question

[ericmajinglong]

If I have a predicted RNA stem-loop of energy -0.30 kcal/mol, and another of -4.9 kcal/mol, how do I tell whether such a structure is a significantly stable structure or not? Our two competing hypotheses are that there is some structure with sufficient energetic stability to fold inside a cell, versus the one that there is not.

Answer 1

[Alex Paciorkowski]

How have you arrived at your predictions? Have you tried using a structure prediction package like RNAstructure? I believe it can give you some parameters to evaluate predicted structures.