I have earlier made a strategy about double sameturning GC-pairs. Penalizing if there is too many.
This does not take into account the placements of these double blocks of GC-pairs. It is my experience, that they seem to make trouble if connected to a multiloop, as in this Eterna ensemble Shape test design (97%) design 05, sparse 5.
The GC-pair block makes the otherwise stable and correct turning GC-pair in the multiloop, unstable. GC-pairs in blocks gets higher free negative energy, and higher free negative energy is often stabilizing. But having two GC-pairs turning the same way, makes the string they are on, bond less. A string gets stronger, if basepairs are flipped, compared to each other.
For this strategy, I define multiloops as multiloops having three or more strings. (In multiloops with two strings double GC-pairs is allowed in connection to loop ring.)
Also the multiloop should have at least 1 or more nucleotide between the GC-basepairs in the multiloop ring.
I would like to ban sameturning double GC-pairs, if connected to multiloops.
Give -2 pr each.
Neck area is exception to the rule for banning GC’ blocks at multiloops. Here sameturning double GC-pairs are allowed at multiloop end of the neck.