How does the natural fold algorithm work?

How does the natural fold algorithm work? What is it doing to determine how the RNA will fold - does it do permutations to find the lowest energy state? What other factors are involved? As an aside, when in target mode and you are on one side of the RNA puzzle and trying to turn the section from red to white (i.e. stabilized) and then some other section or sections turn red, what is the algorithm doing here to determine this effect? I understand the basic principles of what we are doing but I am interested in how the algorithms work. THANKS!

Is it also that he natural fold takes a linear string of RNA bases and then folds as opposed to the target mode which is working purely at the end state?

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Well, our scoring algorithm is based on Vienna. You can take a look at some of the stuff we use over here:

Kudos to Nando for the links.

Thanks LFP6 for the links.

For anyone interested a good lecture on the basics of an RNA folding algorithm:…