Table 1 Comparison of experimentally-determined and calculated binding energies for twenty-five HIV-1 protease-inhibitor complexes.
From: Improved prediction of HIV-1 protease-inhibitor binding energies by molecular dynamics simulations
PDB code | Resolution | R-factor | Experimental binding energy (kcal/mol) | Calculated binding energy (kcal/mol) (picosecond time scales) | ||||
|---|---|---|---|---|---|---|---|---|
| Â | Â | Â | Â | no MD | 0.01 | 0.10 | 1.00 | 10.00 |
1gno | 2.30 | 0.17 | -9.40 | -7.61 | -16.01 | -15.90 | -12.13 | -10.30 |
1hbv | 2.30 | 0.18 | -8.68 | -10.46 | -15.90 | -14.85 | -12.44 | -10.64 |
1hef | 2.20 | 0.16 | -12.27 | -13.96 | -18.26 | -19.81 | -15.30 | -12.32 |
1heg | 2.20 | 0.19 | -10.56 | -9.15 | -17.77 | -19.41 | -13.39 | -11.16 |
1hih | 2.30 | 0.19 | -10.97 | -9.50 | -17.68 | -17.35 | -14.59 | -11.95 |
1hiv | 2.00 | 0.17 | -12.27 | -11.36 | -23.25 | -21.54 | -19.68 | -17.31 |
1hps | 2.20 | 0.14 | -12.57 | -11.97 | -20.08 | -20.10 | -16.98 | -16.60 |
1hpv | 1.90 | 0.19 | -12.60 | -13.88 | -16.25 | -20.77 | -17.37 | -16.48 |
1hvi | 1.80 | 0.18 | -13.74 | -7.51 | -10.91 | -24.58 | -15.45 | -14.72 |
1hvj | 2.00 | 0.16 | -14.26 | -10.19 | -24.37 | -23.58 | -16.49 | -14.81 |
1hvk | 1.80 | 0.18 | -13.79 | -11.42 | -20.42 | -21.72 | -17.92 | -14.98 |
1hvl | 1.80 | 0.19 | -12.27 | -9.36 | -17.53 | -21.48 | -16.56 | -13.87 |
1hvr | 1.80 | 0.19 | -12.96 | -14.26 | -23.94 | -23.77 | -19.33 | -16.22 |
1hvs | 2.25 | 0.15 | -14.04 | -7.98 | -22.53 | -18.69 | -16.48 | -14.55 |
1hte | 2.80 | 0.16 | -7.69 | -7.86 | -9.85 | -9.10 | -8.38 | -7.74 |
1htf | 2.20 | 0.19 | -9.31 | -8.31 | -20.36 | -15.89 | -18.28 | -18.87 |
1htg | 2.00 | 0.19 | -11.58 | -12.06 | -19.15 | -19.95 | -17.49 | -15.64 |
1pro | 1.80 | 0.19 | -15.40 | -11.52 | -21.80 | -21.91 | -21.33 | -21.32 |
1sbg | 2.30 | 0.19 | -10.56 | -10.45 | -16.96 | -16.67 | -13.86 | -11.91 |
2upj | 3.00 | 0.14 | -10.10 | -8.00 | -15.90 | -14.99 | -11.74 | -11.18 |
4phv | 2.10 | 0.18 | -12.51 | -13.89 | -22.45 | -20.77 | -17.37 | -16.48 |
4hvp | 2.30 | 0.18 | -8.38 | -9.72 | -17.80 | -14.48 | -9.27 | -8.80 |
5hvp | 2.00 | 0.18 | -8.12 | -8.83 | -17.46 | -16.01 | -9.29 | -8.09 |
8hvp | 2.50 | 0.14 | -12.27 | -8.62 | -20.69 | -20.16 | -18.70 | -16.15 |
9hvp | 2.80 | 0.18 | -11.38 | -12.18 | -20.88 | -19.41 | -18.88 | -15.55 |
Correlation coefficient | 0.38 | 0.53 | 0.87 | 0.79 | 0.74 | |||