Skip to main content

Advertisement

Table 3 Results of docking calculations using semi-empirical charges on both the ligand and the protein.

From: Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock

PDB code of the complex RMSD of the first rank result as compared to the X-ray (Å) Energy rank of the lowest RMSD hit Frequency rank/frequency of the best geometry Lowest RMSD (Å) Estimated free energy of binding (kcal/mol) Experimental binding energy (kcal/mol)
1AI5 1.22 1 1/100 0.65 -5.06 -5.08
1AJP 2.73 2 1/97 1.07 -4.82 -3.05
1AMW 2.13 1 1/35 0.87 -5.67 -6.19
1BGQ 1.03 1 1/100 0.70 -6.50 -11.69
1CBR 1.01 1 1/93 0.77 -7.42 -10.58
1D3Q 2.77 2 2/40 0.85 -11.47 -8.88
1D3T 2.09 3 1/60 0.99 -10.37 -8.73
1DWB 0.72 1 1/100 0.54 -4.87 -3.98
1FLR 0.39 1 1/100 0.39 -8.54 -10.98
1GNI 3.01 2 1/69 1.01 -6.80 -11.01
1HVJ 1.61 1 1/5 1.61 -10.45 -14.27
1HVR 1.21 1 1/96 1.00 -11.67 -12.97
1K4G 2.83 4 1/89 1.42 -7.78 -7.99
1KV1 0.6 1 1/100 0.58 -9.33 -8.10
1LIF 3.1 4 3/17 0.93 -4.51 -9.65
1M0N 1.18 1 1/86 1.02 -7.65 -3.03
1M0Q 1.03 1 1/80 0.95 -7.15 -5.30
1OLU 0.89 1 1/89 0.61 -9.14 -6.01
1Q8T 1.9 1 1/100 1.41 -7.58 -6.49
1RBP 0.85 1 1/100 0.56 -8.46 -9.17
1S39 4.29 2 1/95 0.33 -4.65 -10.50
1U33 0.86 1 1/43 0.80 -9.82 -6.28
1ULB 0.7 1 1/100 0.64 -5.09 -7.20
1UWT 2.35 1 1/53 0.71 -6.47 -8.14
1X8R 1.26 1 1/100 0.96 -3.10 -8.36
1XD1 1.81 1 2/10 1.30 -15.97 -10.80
1YDT 0.79 1 1/93 0.45 -8.05 -9.98
1ZC9 2.7 14 2/26 0.96 -6.76 -4.39
2ACK 3.98 4 2/22 0.94 -5.25 -8.97
2BAJ 0.66 1 1/100 0.55 -12.50 -11.46
2BAK 1.21 1 1/98 0.64 -14.20 -10.14
2CEQ 0.85 1 1/44 0.83 -6.23 -9.92
2CET 2.61 1 2/15 0.96 -7.76 -10.94
2CGR 0.9 1 1/100 0.68 -10.05 -9.89
2CPP 1.21 1 1/100 1.21 -6.26 -8.28
2D3U 0.68 1 1/100 0.54 -7.11 -9.44
2D3Z 3.86 3 1/88 0.63 -7.60 -9.06
2FDP 0.75 1 1/89 0.68 -14.80 -10.35
2G94 1.75 1 3/5 1.45 -8.64 -12.99
2GBP 0.89 1 1/100 0.87 -5.60 -10.37
2IFB 2.05 2 1/55 1.03 -4.99 -7.41
2IWX 0.87 1 1/100 0.55 -6.76 -9.11
2J77 2.01 1 1/93 1.60 -7.62 -6.67
2J78 0.83 1 2/27 0.73 -6.13 -8.75
2QFU 2.74 4 2/37 0.94 -6.29 -5.70
2QWB 4.35 12 2/15 0.90 -6.64 -3.74
2QWD 2.57 2 1/67 0.91 -7.37 -6.62
2R04 1.99 2 2/8 0.92 -8.84 -8.87
2XIS 1.17 1 1/100 1.14 -6.93 -7.94
2YPI 1.19 1 1/61 0.78 -2.62 -6.57
3PTB 1.31 1 1/100 0.74 -5.06 -6.47
4HMG 1.04 1 1/98 0.85 -6.92 -3.48
7ABP 2.09 1 1/97 1.16 -5.58 -8.78
  Average: 1.71 without outliers (rmsd above 4 Å): 1.61 38 first hits 42 first hits Average: 0.87   
  1. QASP parameter was modified from 0.01097 to 0.00679 in AutoGrid and AutoDock. The average value of the RMSD between the lowest energy result and experimental structure and the total number of successful first rank predictions (based on lowest energy and highest cluster population, respectively) are indicated at the bottom of the table.