I’m not able to find what the free energy formula is and parameters are. Although there are some discussions on the forum, I’d like to find a definitive answers.
Just think about any existing RNA secondary structure prediction algorithms, there are many parameters to control the program as well as different parameters to compute the free energy (either minimum or ensemble average).
Could the authors of eterna game provide an official detailed descriptions on how the energy is computed?
The in silico parameters are currently based on what was in ViennaRNA 1.0, which should correspond to Turner99. Indeed we are grateful to the Vienna folks for letting us use their code as a back-engine! This has allowed comparison to several RNA design codebases like Vienna’s InverseRNA method, infoRNA, and RNA-SSD.
In the near future, we will allow more updated thermodynamic models (e.g. in Vienna 2.0 or the Mathews 2004 parameters that are used in RNAstructure), especially for designs that will be candidates for lab synthesis.
It’s restricted. Where’s the PDF file?
I found it here (the title says 2003, but its the 1999 paper):