A hierarchical docking method: XDZ_2
OMEGA 2.5/SHAFTS/MGLTools/AutoDock Vina 1.0/ITScore2
maxconfs=500 #OMEGA
Gasteiger charges #Vina
All the released crystal structures of human CatS
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
Re-scoring function, ITScore2 #ITScore version 2.0
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 FXR structures. The protein structure in the PDB entry
that has the best similarity score with the query ligand was used for docking.
Then, a modified version of AutoDock Vina was used for the sampling, outputting up to 500 binding
models for further evaluation. A knowledge-based scoring function, ITScore2, was used to
evaluate these binding models. The scoring function was developed with a statistical
mechanics-based iterative method using the refined set of PDBbind 2012.
No
Yes