Pseudoknot score

The dev’s might think about creating a single score from the Pair Probability Plot to show when the pseudoknot(s) are sufficiently balanced with the stacks to score well. Solving a pseudoknot puzzle
is pretty easy but balancing stack energy and pseudoknot energy is another.


You will get to test this idea in a few weeks when we get the first batch of pilot results. I recall both jandersonlee and jennifer pearl discussing this idea as well. Not the specific idea of creating a metric, but the energy balance between the two stems.

The researchers likely will apply machine learning to develop a new algorithm, or maybe a metric, that could be cool, because machine learning supposedly will take all factors, such as energy balancing, into account at once. I’m not convinced it always works and I could be misstating the concept.