Table 2.
The roles of different energy items in the scoring function
| %χ1 correct | %χ1+2 correct | |||||||||||
| Van der waalsa | Surface and volume | Backbone dependency | Electrostatic energy | Desolvation energyb | ACEc | Sphi and Sphod | Average rms deviation | Overall rms deviation | All | Core | All | Core |
| + | − | − | − | − | − | − | 1.094 | 1.723 | 79.0 | 91.0 | 60.0 | 79.6 |
| − | + | − | − | − | − | − | 1.003 | 1.619 | 82.5 | 94.0 | 64.3 | 82.5 |
| − | − | + | − | − | − | − | 1.290 | 2.065 | 72.1 | 74.0 | 52.3 | 58.5 |
| − | + | + | − | − | − | − | 0.778 | 1.254 | 89.2 | 95.2 | 74.6 | 86.9 |
| − | + | + | + | − | − | − | 0.741 | 1.211 | 89.9 | 95.2 | 77.1 | 87.9 |
| − | + | + | + | + | − | − | 0.714 | 1.175 | 90.4 | 96.0 | 78.3 | 89.1 |
| − | + | + | + | − | + | − | 0.729 | 1.162 | 90.1 | 95.4 | 77.5 | 88.1 |
| − | + | + | + | + | − | + | 0.730 | 1.173 | 90.0 | 95.6 | 77.1 | 88.6 |
a CHARMM Van der Waals potential functions were used. All atom radii were scaled by 0.9 to relieve the errors caused by discrete rotamers.
b The number of completely buried nonhydrogen-bonded polar atoms
c Atomic contact energy (Zhang et al. 1997
d Buried surfaces of hydrophobic and hydrophilic atoms.