Folding is dynamic over the lifetime of the RNA, things like SHAPE are nice but only provide a snapshot. It is still leagues better than simply going by the old school thermodynamics based folding algorithms. A neat way to check out this 'folding space' is to generate all possible structures (possible even for long sequences if you don't include psuedoknots), then do alignments, or integrate experimental data like SHAPE.
Interesting to see this here. Shameless plug: if you want to get a basic idea of how RNA folding algorithms work (without pseudoknots) I wrote a blog post about it:
[+] [-] kusmi|8 years ago|reply
[+] [-] mjfl|8 years ago|reply
http://michaeljflynn.net/2017/01/09/simple-rna-folding-in-13...