Skip to main content

Advertisement

Table 3 Ligand all-atom RMSD (Å) and the number of docking solutions (N) in the cluster from 100 Larmarckian genetic algorithm (LGA) docking runs of twenty-five protease-inhibitor complexes.

From: Improved prediction of HIV-1 protease-inhibitor binding energies by molecular dynamics simulations

PDB No MD 0.01 ps 0.1 ps 1 ps 10 ps
code N RMSD (Å) N RMSD (Å) N RMSD (Å) N RMSD (Å) N RMSD (Å)
1gno 32 0.62 18 0.88 4 1.54 13 1.57 16 1.54
1hbv 4 2.15 8 1.18 6 1.30 6 2.05 9 3.18
1hef 8 1.46 6 1.24 4 1.13 12 2.14 9 2.23
1heg 15 2.16 7 0.88 4 0.94 6 1.31 5* 1.20
1hih 14 1.21 6 0.58 4 0.75 7 1.81 4 3.86
1hiv 12 1.27 8 1.04 4 1.06 5 1.29 7 2.75
1hps 10 1.03 5 1.35 1 0.95 5 1.53 2 2.84
1hpv 3 1.33 9 1.32 5 0.73 5 2.92 7 2.59
1hvi 13 1.53 6 0.93 4 0.95 2 2.94 5 3.54
1hvj 3 1.33 3 0.75 2 0.95 2 2.35 4 2.86
1hvk 8 1.44 4 1.34 7 1.12 9 0.97 2 3.26
1hvl 12 1.72 2 1.61 2 1.54 5 2.49 3 2.92
1hvr 18 0.98 9 0.70 6 0.68 8 1.01 8 2.37
1hvs 13 1.73 7 0.87 1 1.03 3 0.99 3 1.24
1hte 3 2.26 9 1.21 3 1.88 7 2.72 8* 3.23
1htf 13 1.11 8 1.03 6 0.93 13 2.11 10 2.9
1htg 8 1.96 9 0.97 8 1.03 6 0.96 12 2.86
1pro 18 0.76 15 0.78 7 0.77 9 0.63 9 0.87
1sbg 11 1.71 17 0.61 8 0.73 2 1.01 9 2.63
2upj 15 1.75 17 1.74 4 1.79 2 2.07 9 3.54
4phv 1 2.93 9 1.57 3 1.23 3 2.51 7 3.08
4hvp 3 1.97 11 0.98 2 1.37 5 1.91 7 2.16
5hvp 12 1.89 5 0.86 2 0.88 8 0.97 8* 1.01
8hvp 13 1.75 5 1.53 2 1.41 2 2.25 8 2.16
9hvp 6 2.66 6 1.48 2 1.54 2 2.51 8 2.12
Average 10.72 1.63 8.36 1.10 4.12 1.13 5.88 1.80 7.16 2.51
  1. Docking solutions with ligand all-atom RMSDs within 1.0 Å of each other were clustered together and ranked by the corresponding lowest energy representative. The lowest energy solution of the lowest ligand RMSD cluster was accepted as the calculated binding energy. The lowest ligand RMSD cluster was usually ranked as the first cluster; the clusters that were ranked as a second cluster are marked with (*). Average N values from docking results of all MD simulation time scales are lower than an average N value from protein-rigid docking, indicating that the ligands bind to the binding pocket of the MD simulated structures with higher specificity.