Table 1. RMSDs of Docking Poses Generated by CHARMMing’s Fragment-Based Docking Protocol and Glide SP and success Rates (defined by the percentage of the ligands whose reported RMSD is below 2.0 Å)a.
| PDB ID | resolution (Å) | best RMSD (Å) | Glide SP RMSD (Å) |
|---|---|---|---|
| 1A4Q | 1.90 | 2.61 | 3.30 |
| 1A6W | 2.00 | 1.01 | 6.72 |
| 1AOE | 1.60 | 3.13 | 1.80 |
| 1AQW | 1.80 | 1.88 | 0.96 |
| 1ATL | 1.80 | 1.68 | 1.09 |
| 1BMA | 1.80 | 2.76 | 1.55 |
| 1D3H | 1.80 | 0.99 | 0.81 |
| 1FCZ | 1.38 | 1.06 | 0.31 |
| 1GLQ | 1.80 | 4.71 | 1.01 |
| 1HFC | 1.50 | 2.63 | 2.36 |
| 1HVR | 1.80 | 3.84 | 0.75 |
| 1JAP | 1.82 | 1.41 | 0.92 |
| 1KE5 | 2.20 | 1.07 | 1.75 |
| 1MLD | 1.83 | 1.29 | 1.07 |
| 1MMQ | 1.90 | 0.50 | 0.30 |
| 1MTS | 1.90 | 1.96 | 0.54 |
| 1MVC | 1.90 | 0.29 | 0.94 |
| 1NHZ | 2.30 | 0.78 | 1.89 |
| 1NQ7 | 1.50 | 0.94 | 1.26 |
| 1QBR | 1.80 | 9.31 | 0.98 |
| 1SRJ | 1.80 | 1.33 | 0.51 |
| 1TXI | 1.90 | 1.66 | 1.64 |
| 3ERT | 1.90 | 0.71 | 1.59 |
| 4DFR | 1.70 | 1.66 | 10.48 |
| Success Rate: | 71% | 84% | |
a
“Best RMSD” refers to the pose closest to the crystal structure. Glide SP RMSD is of the top scoring pose of Glide’s standard precision docking.