Fig. 1

a, b Illustrations of an exemplary structure S and the respective structure tree. PMcomp energy model is composed of the probabilities of base-pairs, shown with plain black arcs and nodes. Pankov energy model additionally incorporates in-loop probabilities of paired base-pairs that are illustrated with blue arrows. c Top: PMcomp structure model assume independence between the base-pair probabilities by multiplying the probabilities. Bottom: Pankov uses a loop-aware scheme to compute the probability of the structure that is efficiently calculated from pre-computed loop-conditional probabilities \(P(a \Vert a')\) based on the parent-child relation of the base-pairs