Jon, after having taking Physical Chemistry and dropped it when my mother became terminally ill, I would guess that they are using Molecular Physics, which incorporates Quantum Physics by necessity . They are multiple ways a protein can fold, but only one typically works biologically. Mad Cow occurs when a brain protein isn't folded right any more! So determining first why it folds, and then making sure it folds that way, is cutting edge biology and physics - Biophysics (?).
these are basically conformers, but you have to calculate energy levels, and energy thresholds on a multitude of ways, and also you take into consideration that there are "paths" of folding, you get some very difficult.
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