
Predicting how RNA folds in 2D including Pseudoknots (2013) - slbenfica
https://fermatslibrary.com/s/accurate-shape-directed-rna-secondary-structure-modeling-including-pseudoknots#email-newsletter
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kusmi
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.

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mjfl
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:

[http://michaeljflynn.net/2017/01/09/simple-rna-folding-
in-13...](http://michaeljflynn.net/2017/01/09/simple-rna-folding-in-130-lines-
of-haskell/)

