From: A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures
Name | Description | Value (Kcal/mol) |
---|---|---|
P _{ s } | Exterior pseudoloop | −1.38 |
initiation penalty | ||
P _{ s m } | Penalty for introducing pseudoknot | 10.07 |
inside a multiloop | ||
P _{ s p } | Penalty for introducing pseudoknot | 15.00 |
inside a pseudoloop | ||
P _{ b } | Band penalty | 2.46 |
P _{ u p } | Penalty for unpaired base | 0.06 |
in a pseudoloop | ||
P _{ p s } | Penalty for closed subregion | 0.96 |
inside a pseudoloop | ||
e_{ H }(i,j) | Energy of a hairpin loop closed by i.j | |
e_{ S }(i,j) | Energy of stacked pair closed by i.j | |
e_{ s t P }(i,j) | Energy of stacked pair that | 0.89×e_{ S }(i,j) |
spans a band | ||
e_{ i n t }(i,r,r^{′},j) | Energy of a pseudoknot-free | |
internal loop | ||
e_{ i n t P }(i,r,r^{′},j) | Energy of internal loop | 0.74×e_{ i n t }(i,r,r^{′},j) |
that spans a band | ||
a | Multiloop initiation penalty | 3.39 |
b | Multiloop base pair penalty | 0.03 |
c | Penalty for unpaired base | 0.02 |
in a multiloop | ||
a ^{′} | Penalty for introducing a multiloop | 3.41 |
that spans a band | ||
b ^{′} | Base pair penalty for a multiloop | 0.56 |
that spans a band | ||
c ^{′} | Penalty for unpaired base in a multiloop | 0.12 |
that spans a band |