Table 4.
MM-PBSA results compared to experimental binding parameters.
| Complex | Binding parameters | MM-PBSA energy terms (KJ/mol) | ||||||
|---|---|---|---|---|---|---|---|---|
| Kon/105 (M−1 s−1) | Koff/10−5 (s−1) | KD (pM) | ΔEbinding | ΔEVdW | ΔEelectrostatic | ΔGPolar | ΔGApolar | |
| Ranibizumab/VEGFA | 1.60 | 0.73 | 46 | −7.0±40 | −4.8±5 | −1.0±20 | 410 ± 30 | −5.2±7 |
| Fab-bevacizumab/VEGFA | 5.30 | 3.10 | 58 | −8.7±30 | −3.2±10 | −2.2±20 | 343 ± 30 | −5.6±7 |
| VEGFR1d2_R2d3/VEGFA | 410 | 2.01 | 0.49 | −14.0±90 | −3.7±50 | −14.3±1.0 | 1050 ± 100 | −7.0±40 |
Kinetic and binding parameters are from Papadopoulos et al. (2012).