Table 8.
Assessment of the ability of the PHOENIX scoring function to classify complexes into three binding affinity groups: low-affinity (pKd < 5.0), medium-affinity (5.0 ≤ pKd ≤ 8.0), and high-affinity (pKd > 8.0). The number of correctly categorized complexes and total number of complexes in each category, as well as the percentage of the correctly categorized complexes are presented for PHOENIX and the commonly used scoring functions take from the Wang et al. study26 for comparison purposes.
| Scoring Function | Low | Medium | High |
|---|---|---|---|
| PHOENIX | 52/205=27% | 417/417=100% | 112/193=61% |
| SFSscore::met | 88/191=46% | 309/417=74% | 86/192=45% |
| X-Score::HPScore | 33/205=16% | 358/402=89% | 48/193=25% |
| X-Score::HMScore | 41/205=20% | 348/402=87% | 65/193=34% |
| X-Score::HSScore | 29/205=14% | 350/402=87% | 53/193=27% |
| DrugScore::Pair | 24/205=12% | 359/402=89% | 45/193=23% |
| DrugScore::Surf | 11/205=5% | 362/402=90% | 45/193=23% |
| DrugScore::Pair/Surf | 24/205=12% | 358/402=89% | 47/193=24% |
| Sybyl::D-Score | 0/205=0% | 384/402=96% | 2/193=1% |
| Sybyl::PMF-Score | 0/196=0% | 395/396=99% | 0/193=0% |
| Sybyl::G-Score | 12/205=6% | 359/402=89% | 30/193=16% |
| Sybyl::ChemScore | 38/204=19% | 349/400=87% | 40/193=21% |
| Sybyl::F-Score | 0/182=0% | 362/362=100% | 0/188=0% |
| Cerius2::LigScore | 11/186=6% | 340/366=93% | 16/165=10% |
| Cerius2::PLP1 | 24/205=12% | 364/401=91% | 35/193=18% |
| Cerius2::PLP2 | 30/205=15% | 363/402=90% | 32/193=17% |
| Cerius2::PMF | 0/202=0% | 390/400=97% | 3/193=2% |
| Cerius2::LUDI1 | 1/203=0% | 379/394=96% | 9/193=5% |
| Cerius2::LUDI2 | 6/205=3% | 378/401=94% | 15/193=8% |
| Cerius2::LUDI3 | 1/205=0% | 387/402=96% | 9/193=5% |
| GOLD::GoldScore | 0/178=0% | 331/339=98% | 4/177=2% |
| GOLD::GoldScore_opt | 3/200=1% | 366/385=95% | 11/187=6% |
| GOLD::ChemScore | 8/177=5% | 345/376=92% | 37/188=20% |
| GOLD::ChemScore_opt | 20/187=11% | 346/386=90% | 38/189=20% |
| HINT | 2/205=1% | 388/402=97% | 11/193=6% |