Definition: Asymmetic multiloop = multiloop with different numbers of nucleotides between the multiloop arms. The asymmetry lab design is an example of this design type.
Most of the rules we found were working in the symmetric designs are the same in the asymmetric designs (designs with asymmetric arms or mulotiloops). But some of the rules seem to be a bit sloppier in the asymmetric designs.
This is why I would like a strategy specificly for tetraloop similarity in designs with asymmetric multiloop. In symmetric designs energy level in tetraloop is preferable the same in all tetraloops or at least a tetraloop have an energy twin.
In the asymmetry design the tendency is the same, but differences of 0.2 to 0.4 appears to be okay.
So this strategy should only be run for designs with asymmetric multiloops and not vote on usual symmetric designs.
I would like a strategy that ad points for having similar energy content in tetraloops
For designs with 2 tetraloops:
If energy in all tetraloops are similar in energy content, ad 5 points
If the energy in the two tetraloops are 0.2 different ad 5 points
If the energy in the two tetraloops are 0.4 different ad 5 points
If the energy difference between the two tetraloops are higher, penalize with -1, per 0.5 rise in energy difference between the tetraloops.
I assume the same tendency will be present in designs with asymmetric multiloops, but more arms.