It is fully possible to break the pattern with similar tetraloop energy. I tried it myself in several cloud lab designs on purpose.
I want to adjust my strategy as I see a clearer picture arise. My first strategy is not fully wrong, it is just possible to get around it if the stems in the design are stable enough to hold the loop. And in particular if the design has longer stems. However even in the long stem designs there is a tendency for more loops with uneven energy in the loops among the lower scoring.
Where I see more of a pattern now is for designs with shorter stems on a multiloop. There is a higher prevalence of uneven energy distribution in end loops for the lower scoring designs than among the winners. It is still fully possible to break pattern. But still there is a tendency, but I think it will be more outspoken in designs with 4 bp stems and shorter. This should be reflected in the strategy, for the best use of it.
Give double penalty in stems 4 bp and shorter if for uneven energy in same size end loops. The bigger the difference, the worse. Also I believe there is an optimal energy range for each size loop.
I think if stems are well constructed and in themselves stable, it has a chance, even though the loops are very different in energy. However if the stems has some instabilities, too different loop energies, will tip the cardhouse. I think this goes too in bigger end loops. Though a certain percentage in energy difference is allowed.
Hyphema found another of the exceptions in the Half branches lab, in designs by Merriskies and wondered.
Hyphema: been looking more at the Half of the Branches lab and have no idea why Merriskies scored so high with the exception that the tetraloops were so asymmetric energetically
Hyphema: thankfully merriskies had another similar design synthd and it did poorly and the big difference was the boosting of the tetraloop
Eli Fisker: Uneven energy in tetraloop is allowed
Hyphema: but was that the key?
Hyphema: or just some fluke?
Eli Fisker: but I think it generally goes better for designs with long stems
Hyphema: certainly that
Eli Fisker: Usually this goes worse in designs with shorter stems
Eli Fisker: However I think it flies as the two stems are quite different
Here are the designs that Hyphema was thinking about: http://eterna.cmu.edu/game/browse/742…
I’m still not sure that what I say about loop energy similarity is the full truth, but I think it is closer to the truth this time. It will be interesting to see what it end up with.