How is the estimated mode secondary structure computed from the SHAPE data?

Is this handled in the energy model, or is there some custom code taking care of this?

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You won’t find anything related to SHAPE (or any other chemical mapping for that matter) in any NN parameter sets. This said, some RNA folding package writers did code things themselves. I believe RNAStructure was the first, and I think I heard that Vienna 2.2 will include a similar functionality. Eterna’s algorithm for that function was implemented by Jee, and yes, like the ones I just mentioned, it’s custom.

If ViennaRNA v. 2.2 integrates the ability to compute SHAPE directed secondary structure predictions, will you be adding that function into Eterna as an option for players, or possibly to replace Jee’s custom code?

Eventually, but this is evidently quite low priority at the moment. Also, I would require to be convinced that these calculations actually are superior to Jee’s algorithm, in particular, that they attempt to interpret the SHAPE data as the result of global effects on the whole ensemble. If that’s the case, and as soon as I don’t have anything better to do (my todo list is still long), I will look into it.