Energetically best pseudoknots might be deeply buried under suboptimal solutions. To make them visible we could apply a binary classification algebra. One class for nested structures, the other class for pseudoknots. Here, we want to differentiate between four classes, namly
isH
and isK
. The only affected rules are cadd
, pknot
and pkiss
.
An application of enforced pseudoknot computation is e.g. KnotInFrame.