Table 6.
The SCARE docking results (the pocket boundaries are defined by all the residues within ~5 Å from the ligand experimental pose).
| Protein | Receptor PDB | Ligand PDB | First Near Native RMSD (Å) a | First Near Native Rank |
|---|---|---|---|---|
| AR | 2ACR | 2FZB | 1.3 | 1 |
| Anti-Steroid Fab’ | 1DBA | 1DBB | 0.6 | 1 |
| CDK2 | 1AQ1 | 1DM2 | 0.6 | 1 |
| 1DM2 | 1AQ1 | 1.4 | 1 | |
| COX-2 | 1CX2 | 3PGH | 0.8 | 1 |
| 3PGH | 1CX2 | 0.9 | 1 | |
| ER | 1ERR | 3ERT | 2.0 | 1 |
| 3ERT | 1ERR | 1.5 | 1 | |
| Factor Xa | 1KSN | 1XKA | 1.2 | 1 |
| 1XKA | 1KSN | 0.6 | 1 | |
| GSK-3 β | 1Q4L | 1UV5 | 0.8 | 1 |
| 1UV5 | 1Q4L | 1.8 | 5 | |
| Hiv1 RT | 1C1C | 1RTH | 1.0 | 6 |
| 1RTH | 1C1C | 1.1 | 1 | |
| JNK3 | 1PMN | 1PMV | 0.9 | 1 |
| 1PMV | 1PMN | 1.1 | 1 | |
| LXR β LBD | 1P8D | 1PQ6 | 1.8 | 1 |
| 1PQ6 | 1P8D | 1.3 | 1 | |
| Neuroaminidase | 1A4Q | 1NSC | 1.4 | 1 |
| 1NSC | 1A4Q | 0.6 | 1 | |
| P38 Kinase | 1BMK | 1DI9 | 1.2 | 3 |
| 1DI9 | 1BMK | 1.6 | 1 | |
| PKA | 1STC | 1YDS | 1.2 | 1 |
| 1YDS | 1STC | 0.7 | 1 | |
| PPARγ | 1FM9 | 2PRG | 1.8 | 1 |
| 2PRG | 1FM9 | 1.3 | 1 | |
| TK | 1KI4 | 1KIM | 1.3 | 1 |
| 1KIM | 1KI4 | 0.6 | 1 | |
| Trypsin | 1PPC | 1PPH | 0.6 | 1 |
| 1PPH | 1PPH | 1.7 | 1 |
a
RMSD value and rank of top scoring near native conformations are reported in bold. A near native solution predicted as the top best rank in 90%, within six top ranks in 100%.