I would like a strategy that says, no red nucleotide, if not paired up with green nucleotide in a GC-pair or at boostpoint position.
For each red nucleotide not paired up with green (alone – placed in outer loops, internal loops, multiloop, bulges and hookarea, give -1 pr. each.
That is unless if placed at boostpoint position. Boostpoint - expression Iroppy uses for placing red or green nucleotides in multiloop ring or hook area, at first position to right or left in a loop, where it raises the level of negative energy inside and stabilizes the structure.
If placed at boostpoint position give -0,5 pr. each.
We are glad to report that your strategy has been implemented and tested.
While implementing your strategy, we have made small changes to the parameters you specified to optimize the performance.
Note that we’ll always run a optimization over the parameters you specify, so you won’t have to worry about fine tuning all the numbers you use.
Just the idea and rough numbers are enough to run your algorithm!
Length : Your strategy was implmented with 38 line of code.
Ordering : We ran your strategy on all synthesized designs and ordered them based on predicted scores. The correlation of your strategy’s ordering with the ordering based on the actual scores was 0.218727089833. (1.0 is the best score, -1.0 is the worst score. A completely random prediction would have 0 correlation)
Please note that the numbers specified above will change in future as we’ll rerun your algorithm whenever new synthesis data is available.
Hmm, Just curious if *not* penalizing stack internal GU prior to CG or stack internal GU prior to GC would change the scoring? That is G paired with U where the G is immediately followed by either C paired with G or G paired with C, where the GU does not occur at the end of a stack. GU followed by CG is a relatively strong stack cell (-2.5 kcal) and so is GU followed by GC (-2.1 kcal).
I think “un-penalizing” GU-pairs will change the scoring. Propably for a bit lower. That strategy will also catch some of the legally placed GU-pairs. You could make it a strategy.
JL, you read my strategy correct, there is no legal places for GU’s in it. I was playing along with your idea on what would happen, if there were. Good luck.