Pseudoknot energy models have been studied in more detail in the past years and reliable energy parameters are in high demand. It is widely accepted that pseudoknot energy cannot be estimated with an additive model as used in MFE folding. There is strong interference between opposite loops and stems (L 1 and S 2 , L 3 and S 1 ), which come in close contact in the 3D fold. In a simple hairpin type (H-type) pseudoknot, loops L 1 and L 3 span across the deep narrow (major) groove and the shallow wide (minor) groove, respectively. The corresponding loop entropies are, therefore, not equivalent and depend on the structure and length of the opposite stem (41, 42) .