Table 2 Performance of structure-based virtual screening on various receptor models.
| Â | MSM with TT | MSM with NT | Standard AF2 | Crystal structure | AlphaFold3 | |||
|---|---|---|---|---|---|---|---|---|
ADB | BW | ADB | BW | ADB | BW | |||
DUD-E Kinase Subset (25 proteins) | ||||||||
 EF1% | 7.2 | 7.2 | 8.2 | 8.0 | 6.6 | 7.8 | 6.5 | 6.9 |
 EF5% | 3.5 | 3.7 | 3.7 | 3.7 | 3.5 | 4.0 | 3.4 | 3.5 |
 EF10% | 2.7 | 2.7 | 2.6 | 2.7 | 2.6 | 2.9 | 2.7 | 2.7 |
 AUC | 0.660 | 0.639 | 0.661 | 0.664 | 0.659 | 0.672 | 0.664 | 0.664 |
 BEDROC | 0.193 | 0.196 | 0.183 | 0.189 | 0.183 | 0.206 | 0.184 | 0.185 |
Average Dissimilarity ≥ 0.7 (14 proteins) | ||||||||
 EF1% | 5.3 | 5.6 | 6.4 | 6.9 | 4.6 | 5.3 | 4.5 | 4.8 |
 EF5% | 3.0 | 3.1 | 3.2 | 3.2 | 2.8 | 3.4 | 2.7 | 2.9 |
 EF10% | 2.4 | 2.4 | 2.2 | 2.3 | 2.1 | 2.6 | 2.3 | 2.4 |
 AUC | 0.646 | 0.652 | 0.648 | 0.650 | 0.641 | 0.667 | 0.647 | 0.648 |
 BEDROC | 0.166 | 0.171 | 0.154 | 0.161 | 0.146 | 0.175 | 0.148 | 0.151 |
Average dissimilarity < 0.7 (11 proteins) | ||||||||
 EF1% | 9.6 | 9.3 | 10.6 | 9.3 | 9.1 | 10.9 | 9.1 | 9.5 |
 EF5% | 4.2 | 4.4 | 4.4 | 4.3 | 4.3 | 4.8 | 4.3 | 4.4 |
 EF10% | 3.0 | 3.1 | 3.1 | 3.1 | 3.3 | 3.3 | 3.2 | 3.2 |
 AUC | 0.678 | 0.681 | 0.678 | 0.681 | 0.681 | 0.679 | 0.685 | 0.685 |
 BEDROC | 0.228 | 0.228 | 0.220 | 0.226 | 0.229 | 0.245 | 0.229 | 0.228 |
