Table 1.
Terphenyl-CaM interaction energy (in kcal/mol) predicted by the methods DOCK, AMMOS, GBSA, X-Score for the top scored poses
| RMSD (Å) | DOCK vdw + es | AMMOS vdw + es | GBSA vdw + es | X-Score | ||
|---|---|---|---|---|---|---|
| Receptor structure No pose | before AMMOS refinement | after AMMOS refinement | ||||
| 1CLL | ||||||
| 1 | 3.3 | -48.63 | -14.90 | -26.09 | -52.53 | 5.95 |
| 2 | 4.8 | -48.27 | -9.71 | -26.72 | -61.12 | 6.31 |
| 3 | 3.0 | -48.15 | -18.32 | -29.91 | -56.85 | 6.38 |
| 2K0F model 31 | ||||||
| 1 | 1.9 | -42.70 | -13.04 | -36.42 | -40.05 | 6.78 |
| 2 | 8.8 | -41.70 | -12.64 | -26.45 | -46.17 | 6.68 |
| 2K0F model 76 | ||||||
| 1 | 4.5 | -48.12 | -4.24 | -22.43 | -31.43 | 6.24 |
| 5 | 3.3 | -45.71 | -20.72 | -34.51 | -46.11 | 6.86 |
| 8 | 3.1 | -44.68 | -20.23 | -30.63 | -49.13 | 6.81 |
| 2K0F model 98 | ||||||
| 1 | 8.8 | -49.79 | 3.37 | -16.05 | -21.64 | 6.14 |
| 16 | 7.9 | -38.89 | 5.71 | -17.65 | -23.62 | 5.77 |
| 17 | 7.4 | -38.32 | 48.93 | -4.83 | -31.53 | 6.34 |
| 2K0F model 156 | ||||||
| 1 | 8.2 | -50.52 | -6.90 | -13.17 | -34.42 | 4.31 |
| 6 | 2.3 | -45.57 | -13.08 | -36.31 | -48.90 | 4.69 |
| 12 | 2.5 | -43.51 | -19.25 | -34.35 | -49.93 | 4.89 |
| 2K0F model 160 | ||||||
| 1 | 8.7 | -41.13 | 3.15 | -4.23 | -40.65 | 4.81 |
| 2 | 5.3 | -40.57 | 1.36 | -6.20 | -49.48 | 4.64 |
| 19 | 2.3 | -19.66 | 43.66 | -41.25 | -38.44 | 5.03 |
The column 2 shows the RMSD of the poses as predicted by DOCK.