Maybe im blind but i spent 2 hrs trying to find exact description of rules. I found this tutorial https://www.youtube.com/watch?v=Z-09sAvqXgc&feature=youtu.be which makes think a bit clearer than what is covered by first level of lessons here built in the game. However even there, in the tutorial video things are not explained in details. Can you show me where i can find :
How energy is calculated, to exactly know how boosting works, i mean math formula that give the loop returns energy.
For some energy related reasons its not enough to have bond pairs in stack to be sure map is not red and puzzle is solved. Any chance for link of math formula responsible for that?
Would be nice to have link to some theoretical paper that shows that game is indeed good model for RNA
Eterna uses a handful of what are called “energy models” or “folding engines” to predict what structures a given sequence will fold in to. Integrated into our game are: Vienna 1.8.5, Vienna 2.1.8, NUPACK 3.0.4, EternaFold (a version of CONTRAfold trained on Eterna data), and Linearfold (using Vienna2, CONTRAfold, and EternaFold parameters). Vienna and NUPACK use thermodynamic “nearest neighbor” parameters (IIRC Turner 1999 for Vienna1, and Turner 2004 for Vienna2 and NUPACK. Contrafold and Eternafold are machine-learning-based/probabilistic models. https://rna.urmc.rochester.edu/NNDB/index.html is a good reference for the nearest neighbor rules (though there is some subtle differences in how the engines actually implement them.
For a more approachable introduction to Eterna’s gameplay/dynamics, I highly suggest giving A Gamer's Guide to Eterna by player rna-key a read!
Let me know if there’s any other clarification I can provide
