In it, it is mentioned that there is a special energy bonus for hairpin loops closed with a GU pair, where the G in the pair is preceded by two G residues in base pairs, and an energy penalty for 3 nucleotide hairpin loops that are all C’s. This got me wondering if there are certain aspects in the model which were changed, as it is from 1999, or if certain bonuses and penalties were left out because they did not seem relevant to the game. An answer to this would be much appreciated. Thanks for the game
I think we discussed this in chat after the post, but here’s my answer again.
There are many RNA packages that make use of thermodynamic model and parameters from 1999 paper. However, there are many different settings under which the model can be used. Use of special penalties for GU, consecutive Gs are one of them. Even tetraloop is just an “option.”
As for us, we are using the most standard setting that gets shipped with RNAInverse package.
