Table 3 |
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|
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. |
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|
PDB |
No MD |
0.01 ps |
0.1 ps |
1 ps |
10 ps |
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|
|
|
|
|
|
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|
code |
N |
RMSD (Å) |
N |
RMSD (Å) |
N |
RMSD (Å) |
N |
RMSD (Å) |
N |
RMSD (Å) |
|
|
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|
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 |
|
|
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|
Average |
10.72 |
1.63 |
8.36 |
1.10 |
4.12 |
1.13 |
5.88 |
1.80 |
7.16 |
2.51 |
|
|
||||||||||
|
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. |
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|
Jenwitheesuk and Samudrala BMC Structural Biology 2003 3:2 doi:10.1186/1472-6807-3-2 |
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