Table 3.
Average RMSD values of ligand and protein backbone atomic positions throughout four independent 10 ns molecular dynamics simulation production runs of the four investigated systems: curcumin in complex with PDE4D, 6-gingerol in complex with PDE4D, capsaicin in complex with PDE4D, and resveratrol in complex with PDE4D.
| MD Simulation Run | Production Run 1 |
Production Run 2 |
Production Run 3 |
Production Run 4 |
Average of All Runs |
|---|---|---|---|---|---|
| Curcumin | |||||
| Average ligand RMSD (Å) | 0.93 | 0.87 | 0.88 | 0.99 | 0.92 ± 0.08 |
| Average backbone RMSD (Å) | 0.69 | 0.75 | 0.68 | 0.72 | 0.71 ± 0.08 |
| 6-Gingerol | |||||
| Average ligand RMSD (Å) | 1.53 | 1.82 | 1.72 | 1.90 | 1.74±0.16 |
| Average backbone RMSD (Å) | 0.76 | 0.68 | 0.72 | 0.71 | 0.72 ± 0.11 |
| Capsaicin | |||||
| Average ligand RMSD (Å) | 1.95 | 1.83 | 2.10 | 2.08 | 1.99 ± 0.14 |
| Average backbone RMSD (Å) | 0.71 | 0.82 | 0.81 | 0.81 | 0.78 ± 0.11 |
| Resveratrol | |||||
| Average ligand RMSD (Å) | 0.47 | 0.35 | 0.36 | 0.43 | 0.40 ± 0.04 |
| Average backbone RMSD (Å) | 0.58 | 0.63 | 0.67 | 0.64 | 0.63 ± 0.07 |
The average values of all production runs are presented as mean ± standard deviation.