Name

A hierarchical docking method: XDZ_1

Software

Maestro/OpenEye/MGLTools/AutoDock Vina

System Preparation Parameters

Gasteiger charges

System Preparation Method

All the released crystal structures of human BACE1
proteins bound with small molecules were collected from the Protein Data Bank.
Ligand structures were prepared using the program Maestro.
Preparation for docking with Vina was done using MGLTools.

Pose Prediction Parameters

Exhaustiveness=30 #exhaustiveness of global search (default=8)
Vina scoring funtion
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 BACE1 structures. The PDB entry that has the best similarity score with
the query ligand was used as the template. The program Maestro was employed to build a complex structure, which was then used as the initial structure for Vina docking.

Answer 1

Yes

Answer 2

Yes

Name

BACE1_CNNScore

Software

Tensorflow

Parameters

grid = 32 * 32 * 32

Method

A convolutional neural networks scoring function, BACE1_CNNScore,
was used to evaluate these binding models. The model was originally developed
using the released BACE1-ligand structures and their corresponding binding affinities.

Answer 1

Yes

Answer 2

Yes