Table 5 Molecular docking parameters of HIV-1a-TLR-3 and HIV-1b-TLR-3 complexes
Parameter | HIV-1a | HIV-1b | ||
|---|---|---|---|---|
Before refinement | After refinement | Before refinement | After refinement | |
HADDOCK score | -82.3 ± 26.8 | -241.6 ± 7.2 | -70.4 ± 26.8 | -179.5 ± 2.7 |
Cluster size | 6 | 20 | 5 | 20 |
RMSD from the overall lowest energy structure | 1.0 ± 0.7 | 0.6 ± 0.3 | 0.9 ± 0.5 | 0.6 ± 0.3 |
Van der Waals energy | -57.9 ± 15.8 | 80.2 ± 7.7 | -86.7 ± 3.5 | -95.2 ± 3.7 |
Electrostatic energy | -643.0 ± 93.1 | -788.5 ± 41.5 | -358.3 ± 76.1 | -320.2 ± 23.7 |
Desolvation energy | -1.8 ± 3.8 | 3.6 ± 1.4 | -17.9 ± 1.4 | -20.3 ± 5.3 |
Restraints violation energy | 1059.9 ± 181.2 | 0.0 ± 0.0 | 1058.0 ± 232.6 | 0.0 ± 0.0 |
Buried surface area | 2812.3 ± 177.3 | 3119.2 ± 68.0 | 3320.6 ± 184.1 | 3329.5 ± 71.9 |
Z-score | -1.4 | 0.0 | -1.1 | 0.0 |