Table 7 Free energy parameters for internal loops.
From: Computational RNA secondary structure design: empirical complexity and improved methods
Parameter | Explanation | Values |
|---|---|---|
ΔG-length-I(n) | Destabilizing energy of internal loop of size n (n = 4, 5, 6,...) | 1.7, 1.8, 2.0,... |
ΔG-length-B(n) | Destabilizing energy of bulge of size n (n = 1, 2, 3,...) | 3.8, 2.8, 3.2,... |
ΔG-Internal-n (s i , s j , si+1, sj-1) | Terminal mismatch free energy of closing base pair (s i ·s j ) and neighbouring free bases si+1and sj-1 | -1.1, -0.7, -0.4, 0.0 and 0.7 |
ΔG-Asymmetry(l1, l2) | Penalty for asymmetric internal loops |
|