Table 1.
Summary of the simulations performed.
| Ligand | MD approach | # Replicas | Total simulated time♦ |
|---|---|---|---|
| BnOCPA | SuMD | 6 | 1.9 μs |
| BnOCPA | SuMD-Metadynamics | 5 | 4.3 μs |
| HOCPA | SuMD | 5 | 3.4 μs |
| BnOCPA (bound state after dynamic docking) | Metadynamics | 3 | 0.75 μs |
| BnOCPA(A) | Classic MD | 6 | 9.0 μs |
| BnOCPA(B) | Classic MD | 6 | 9.0 μs |
| BnOCPA(C) | Classic MD | 3 | 3.0 μs |
| BnOCPA(D) | Classic MD | 6 | 9.0 μs |
| HOCPA | Classic MD | 4 | 8.0 μs |
| PSB36 | Classic MD | 4 | 6.0 μs |
| Apo A1 | Classic MD | 4 | 8.0 μs |
| GαCT Goa (BnOCPA) | SuMD + Classic MD | 10 | 0.36 μs + 3.0 μs |
| GαCT Gob (BnOCPA) | SuMD + Classic MD | 10 | 0.33 μs + 3.0 μs |
| GαCT Gi2 (BnOCPA) | SuMD + Classic MD | 10 | 0.37 μs + 3.0 μs |
| GαCT Gob (HOCPA) | SuMD + Classic MD | 10 | 0.29 μs + 3.0 μs |
| BnOCPA(D):Gob | Classic MD | 4 | 4.0 µs |
| BnOCPA(B):Gob | Classic MD | 3 | 3.0 µs |
| HOCPA:Gob | Classic MD | 4 | 4.0 µs |
| BnOCPA(D):Goa | Classic MD | 5 | 5.0 µs |
| BnOCPA(B):Goa | Classic MD | 4 | 4.0 µs |
♦For SuMD and SuMD-metadynamics simulations the time is the sum of productive SuMD time windows.
(A), (B), (C) and (D) indicate the respective BnOCPA binding modes.