Table 1.
Molecular dynamics simulations.
| System ID | DNA | No. of Ligand | No. of Run | Drug Initial State | NPT eq. (ns) | NVT (ns) | Total Time (µs) |
|---|---|---|---|---|---|---|---|
| 1 | n/a | 1 | 2 | Free | 1 | 500 | 1 |
| 2 | Duplex(d([GC]10)2) | 0 | 2 | Free | 1 | 500 | 1 |
| 3 | 3(-p-p-p) (1KF1) | 0 | 2 | Free | 1 | 500 | 1 |
| 4 | 3(-lwd+ln) (143D) | 0 | 2 | Free | 1 | 500 | 1 |
| 5 | 3(-p-lw-ln) (2HY9) | 0 | 2 | Free | 1 | 500 | 1 |
| 6 | Duplex(d([GC]10)2) | 1 | 9 + 1 | Free | 1 | 500 + 2000 | 6.5 |
| 7 | 3(-p-p-p) (1KF1) | 1 | 8 + 2 | Free | 1 | 500 + 2000 | 8.0 |
| 8 | 3(-lwd+ln) (143D) | 1 | 9 + 1 | Free | 1 | 500 + 2000 | 6.5 |
| 9 | 3(-p-lw-ln) (2HY9) | 1 | 9 + 1 | Free | 1 | 500 + 2000 | 6.5 |