Hello. I would like to know a little more about the free energy function used to score structures in EteRNA. What is the formula used? Is it in a paper and if so which one? Thanks a lot!
We use a software called ViennaRNA to calculate free energies and the software is built on this paper.
Hi Jeehyung: Thanks a lot for the prompt reply. While it is fun to play with EteRNA I want to try to understand why the changes I make in the structures produce the effects they do. Hopefuly the paper will answer some of these questions.
Also, you can find out a lot by querying the forums for “energy.”