If free energy and melting point are important concepts, why aren’t targets for those parameters included in any of the puzzles?
Thanks for your question.
The reason that there are no puzzles for minimizing or maximizing free energy or melting points is that it has been shown, both from EteRNA results and from scientific literature, that they aren’t good predictors of how a RNA molecule folds.
Take for example the free energy. The prediction for the free energy of a strand of RNA is at it’s best, a very bad prediction. This is because it is essentially an approximation of an approximation or a number of different scientific experiments. There has been some discussion of the scoring function here and here.
And it is a similar issue for the melting point prediction.
Because of this, we decided to not make challenge puzzles that have players try to optimize their solutions for something that we know to be wrong.
Great idea for tutorials, Graavy.