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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)
     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
  1. For each complex, the PDB code, resolution, R-factor, the experimental energy, the lowest binding energy as evaluated by AutoDock before any MD simulation, and the lowest binding energy after MD simulation for four time points (0.01, 0.1, 1, and 10 ps) are shown. The bottom row shows the correlation coefficient between the experimental and calculated energies. Protein-rigid docking produced poor correlation (of 0.38) between the experimental and calculated energies, while the best correlations (of 0.87) were obtained after 0.1 ps MD simulations.