[Strategy Market] AU pairs are indifferent

[Strategy Market] AU pairs are indifferent

Note : This is a submission in the EteRNA Strategy Market

The alignment (parallel or criss-cross or random) of AU pairs does not have a big stability impact for a design when

  • within stacks that are not in junctions or next-to-junctions - of stacks and loops
  • the “string” (or its two halves) is not symmetrical in the sense of aldo’s mismatches ( http://getsatisfaction.com/eternagame… ).

While this is the case the AU pairs can be substituted with the same amount (or that n-1*) of GU pairs, or an appropriate amount of GC pairs. While being plainly useful for the design’s energy, these “indifferent” pairs, or their substitutes, are the most mobile options for tweaking towards better folding-likelihood in my experience.

*to allow for parallel structure.

Dear TLdicey,

Your strategy has been added to our implementation queue with task id 101. You can check the schedule of the implementation here.

Thanks for sharing your idea!

EteRNA team