1.) 3 stacks max. , 2 better
penalize if more than 3 stacks
2.) half of sequence in invariant when folding between states
penalize if entire sequence is folding
strong penalty if is 3 dimensional (it looks like twists and turns during folding)
3.) molecule is partially free in state 1.
minor penalty if molecule is completely bound in state 1
4.) few kinks in both states
penalize if stack not nicely straight (1-1 mismatches ok,1 or 2)
the more stacks are jagged, more the penalty
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Hi JR,
Would you like these to be implemented as 4 separate strategies or as 1 big strategy?
Thanks,
Vineet
Separate , better to see what works. Thanks.
Dear JR,
Your strategy has been added to our implementation queue and we should have it completed within the next two to three weeks. You can check the status of the implementation here.
We will also be uploading the code used to write your strategy on this page if you are interested in reading it later.
After implementing your idea, we will post the direct link to the code here. Then, we will optimize the parameters, and test it. At that point, we will tell you the correlation of how good your strategy was and what the new optimized parameters are.
Thanks for sharing your idea!
Vineet Kosaraju
The EteRNA Team
Dear JR,
I am pleased to announce that preliminary versions of your strategies have been implemented with. Note that the code might slightly change in the future to remove bugs. We will soon work on optimizing your parameters and testing the strategy.
3 stacks max., 2 better: Implemented with 14 lines of code.
half of sequence in invariant when folding between states: implemented with 29 lines of code.
molecule is partially free in state 1: implemented with 17 lines of code.
few kinks in both states: Implemented with 31 lines of code.
Thank you again for sharing your switch strategy!
Vineet Kosaraju
The EteRNA Team