Vina Score
Vina Score
default
Vina Score, using default parameters
No
A hierarchical docking method: XDZ_3
OMEGA 2.5/SHAFTS/MGLTools/AutoDock Vina 1.0
maxconfs=500 #OMEGA
Gasteiger charges #Vina
All the released crystal structures of human JAK2
protein-small molecule complexes were collected from the Protein Data Bank.
Ligand conformational libraries were generated using OMEGA.
The most stable conformation found for each ligand was then used as a starting
point for docking. Preparation for docking with Vina was done using MGLTools,
in which the ligand PDB files generated with OMEGA were converted to the PDBQT
format by assigning partial charges and atom types.
Exhaustiveness=30 #exhaustiveness of global search (default=8)
Vina scoring function (empirical + knowledge-based function)
Num_modes=500 #max number of poses to generate
For a query compound, the SHAFTS program was employed to calculate
its structural similarities (i.e., the shape-feature similarities) with the small molecules
in the released JAK2 structures. The protein structure in the PDB entry
that has the best similarity score with the query ligand was used for docking.
Then, AutoDock Vina was used for the binding mode prediciton.
No
Yes