A hierarchical docking method: XDZ_1
Maestro/OpenEye/ShaEP/MGLTools/AutoDock Vina
Gasteiger charges
All the released crystal structures of human BACE1
protein-small molecule complexes were collected from the Protein Data Bank.
Ligand structure was prepared using the program Maestro or Omega2 in OpenEye.
Preparation for docking with Vina was done using MGLTools.
Exhaustiveness=30 #exhaustiveness of global search (default=8)
Vina scoring funtion (empirical + knowledge-based function)
Num_modes=100 #max number of poses to generate
For a query ligand, the OEChem TK in OpenEye was employed to calcualte ligand similarities
to the small molecules in the released BACE1 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.
Yes
Yes
ITScore2
ITScore
grid = no
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.
Yes
No