0qyrq-LigandScoringProtocol.txt

Name

Vina Score

Software

Vina Score

Parameters

default

Method

Vina Score, using default parameters

Answer 1

No

0qyrq-PosePredictionProtocol.txt

Name

A hierarchical docking method: XDZ_3

Software

OMEGA 2.5/SHAFTS/MGLTools/AutoDock Vina 1.0

System Preparation Parameters

maxconfs=500 #OMEGA
Gasteiger charges #Vina

System Preparation Method

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.

Pose Prediction Parameters

Exhaustiveness=30 #exhaustiveness of global search (default=8)
Vina scoring function (empirical + knowledge-based function)
Num_modes=500 #max number of poses to generate

Pose Prediction Method

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 CatS 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.

Answer 1

No

Answer 2

Yes