Table 2.
Function | success rate (%) |
||||
---|---|---|---|---|---|
RMSD 0.0 Å | RMSD ≤0.5 Å | RMSD ≤1.0 Å | RMSD ≤1.5 Å | RMSD ≤2.0 Å | |
r·m·r·6 | 80 | 85 | 87 | 89 | 92 |
DrugScoreCSD | 77 | 82 | 83 | 85 | 87 |
ITScore | 64b | 67b | 72 | 79 | 82 |
Cerius2/PLP | 52 | 58 | 63 | 69 | 76 |
Cerius2/LigScore | 48 | 58 | 64 | 68 | 74 |
SYBYL/F-Score | 38 | 47 | 56 | 66 | 74 |
DrugScorePDB | 49 | 58 | 63 | 68 | 72 |
Lennard-Jones | 57 | 61 | 65 | 66 | 68 |
Cerius2/LUDI | 23 | 33 | 43 | 55 | 67 |
X-Score | 25 | 33 | 40 | 54 | 65 |
AutoDock | 8 | 19 | 34 | 52 | 62 |
DFIRE | - | - | 37 | 52 | 58 |
DOCK/FF | n/ab,c | 18b | 37 | 47 | 58 |
Cerius2/PMF | 32 | 35 | 40 | 46 | 52 |
SYBYL/G-Score | 13 | 15 | 24 | 32 | 42 |
SYBYL/ChemScore | 7 | 8 | 12 | 26 | 35 |
SYBYL/D-Score | 3 | 3 | 8 | 16 | 26 |
The success rate at each RMSD criterion is the percentage of all protein-small molecule complexes with the best (i.e., lowest) scoring complex having an RMSD to the native conformation within the allowed deviation. The RMSD ≤0.5Å column corresponds to the definition of ‘accurate’ discrimination used in Figure 1.
Huang, S. Personal communication. 15 Feb 2008.
The success rate for DOCK/FF at RMSD 0.0Å is not available as the minimization in DOCK changes the small-molecule position prior to scoring. The r·m·r function outperforms all other functions at distinguishing native and near-native biomolecular interactions from incorrect conformations.