Name

A hierarchical docking method: XDZ_1

Software

Maestro/OpenEye/ShaEP/MGLTools/AutoDock Vina

System Preparation Parameters

Gasteiger charges

System Preparation Method

All the released crystal structures of human CatS
protein-small molecule complexes were collected from the Protein Data Bank.
In addition, the complex structures released in GC3 were also used.
Ligand structure was prepared using the program Maestro or Omega2 in OpenEye.
Preparation for docking with Vina was done using MGLTools.

Pose Prediction Parameters

Exhaustiveness=30 #exhaustiveness of global search (default=8)
Vina scoring funtion (empirical + knowledge-based function)
Num_modes=100 #max number of poses to generate

Pose Prediction Method

For a query ligand, the OEChem TK in OpenEye was employed to calcualte ligand similarities
to the small molecules in the released CatS structures.The PDB entry that has the best similarity score with
the query ligand was used the template. The program Maestro or ShaEP were employed to build a complex structure,
which was then used as the initial structure for Vina docking.

Answer 1

Yes

Answer 2

Yes

Name

ITScore2

Software

ITScore

Parameters

grid = no

Method

A knowledge-based scoring function, ITScore2, was used to evaluate these
binding models. The scoring function was originally developed with a statistical
mechanics-based iterative method using the refined set of PDBbind 2012.

Answer 1

Yes

Answer 2

No