Table 1 Elementary functions in the basic thermodynamic energy model
Function | Description |
|---|---|
sr _energy | The most important source for stabilizing an RNA secondary structure is stacking of two (or more) base pairs. |
termau _energy | A base pair A:U at the terminal end of a stacking region adds less stabilizing energy than within a stacking region. |
hl _energy | Stabilizing contribution for the loop-closing base pair stack plus destabilizing contribution for the hairpin loop region plus bonus energy for special loop sequence (e. g. extrastable tetra loops). |
bl _energy | Analog to hl _energy, but for a destabilizing loop region bulged out to the left. |
br _energy | Symmetric case to bl _energy. |
il _energy | Analog to hl _energy, but with two destabilizing loop regions. |
ml _energy | Since a multiloop of x stems is less stable than x adjacent stems, it gets a penalty. |
ul _energy | Each stem in a multiloop gets an initial penalty. |
ss _energy | Regions of unpaired bases could get penalized, but we set this value to zero. |
sbase _energy | Same as ss _energy, but for a single unpaired base. |