Table 3 Parameter settings used for the execution of the docking process
Setting | Chosen option |
|---|---|
Scoring function | |
Score | MolDock score |
Grid resolution | 0.30Ã… |
Binding site | |
Origin | Volume: 398.336; Surface: 971.52 |
Center | X: 20.73, Y: − 2.48, Z: 35.87 |
Radius | 15 |
Search algorithm | |
Algorithm | MolDock SE |
Number of runs | 10 |
Constrain poses to cavity | Yes |
After docking: Energy minimization | Yes |
After docking: Optimize H-bonds | Yes |
Parameter setting | |
Maximum iteration | 1500 |
Maximum population size | 50 |
Pose generation | |
Energy threshold | 100 |
Simplex evolution | Â |
Maximum steps | 300 |
Neighbor distance factor | 1.00 |
Multiple poses | |
The maximum number of poses returned | 5 |
Enable energy threshold | 0.00 |
Cluster similar poses | RMSD threshold: 1.00 |