some thoughts about the lab puzzles with IUPAC constraints, where shape doesn’t matter as much.
I think we basically have two types of moves available
a) stiffening the loops by putting strong bindings inside
b) loosening up stems to shift the center of gravity and have more favorable loops
also 2 observations:
- in puzzles loops only have few points which are significant for energy change (closing pair, boost points)
- IUPAC constraints allow us only to change roughly every 3rd base (most Aminoacids allow variation in the 3rd base of the codon, only a few [L, S, R] allow changing the first or second base, but these exceptions have internal dependencies which are often difficult to deal with in manual solution exploring. [“if first base is A then third base can’t be U”]
we may want to screen for solutions, where the positions of boost points in loops are divisible by 3, because this would allow us better control of the loops ???