Table 1 Scoring function weights used in the four sampling methods
Weight | Weight | |
|---|---|---|
Score items | (Hard) | (Soft) |
Proling ring closure energy | 1.00 | 1.00 |
Lennard-Jones attractive | 0.80 | 0.80 |
Lennard-Jones repulsive | 0.40 | 0.60 |
Lazaridis-Jarplus solvation energy | 0.60 | 0.50 |
Pair energy | 0.80 | 0.50 |
Reference energy for each amino acid | 1.00 | 1.00 |
In primary sequence | ||
Backbone-backbone hbonds distant | 2.00 | 1.20 |
Backbone-backbone hbonds close | 2.00 | 1.20 |
Hydrogen bond energy | ||
Sidechain-backbone | 2.00 | 1.20 |
Sidechain-sidechain | 2.00 | 1.20 |
Probability of amino acid at phi and psi | 0.50 | 0.32 |
Omega dihedral in the backbone | 0.50 | 0.50 |