1.) high energy positive kink in stack that contains misformed ligend in state 1 stack OK if ligend to be formed in state 2
Plus if kink exists in correct stack
2.) kink in state 1 stack OK where stack splits into interior loop in state 2.
Plus if kinks exist in correct position in stacks in state 1.
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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 just want to confirm that I know what kink means. Are the kinks in the following picture the ones that have a red box around them?
Thanks,
Vineet
A kink can be any pattern that bends the stack. Above is a 1-0 bulge, A better definition might be any bulge that has positive energy associated with it.
Dear JR,
I am pleased to announce that a preliminary version of your strategy has been implemented with 19 lines of code. The code might slightly change in the future to remove bugs, but you can check the current version here. We will soon work on optimizing your parameters and testing the strategy.
Thank you again for sharing your switch strategy!
Vineet Kosaraju
The EteRNA Team