Reward Low Standard Deviation of Free Energy

My strategy would be to try to reward evenness in free energy. Solutions with a low standard deviation would be scored higher.

Others would know the specific numbers better, but as an example, if a design were to have a StDev of 0.4 for the stacks and 2.3 for the loops, it would get a 100. A StDev of 1 for the stacks and 3 for the loops would be near zero.

Interesting. Would that be averaged over the number of cells per stack, or independent of the stack size?

What about varying loop sizes? Triloops generally have a different energy pattern than tetraloops or pentaloops.

Dear Neil,

Your strategy has been added to our implementation queue with task id 140. You can check the schedule of the implementation here.

Thanks for sharing your idea!

EteRNA team

Any update on this? It has been five months…