I was running some of the designs through CenteroidFold and RNAfold mentioned at http://eternagame.wikia.com/wiki/List…, and the result were very different from the 2nd state for both of the labs I tested. How much of a difference does that aptamar and the FMN molecule make?
Also, I saw some weird things like a loop with a single G on one side and *7* bases on the other side. Seems like there is something major missing from the EteRNA simulation.