1479-1-2tiem-PosePredictionProtocol.txt

Name

3D similarity pose-picking

Software

Smina/Data-Warrior4.7.2

System Preparation Parameters

vinardo scoring function was used in the pose generation

System Preparation Method

First, the 154 test ligands were compared to the 20 published BACE ligands to find the most similar pair. Second, smina vinardo was excuted to dock the 154 test ligands.

Pose Prediction Parameters

Vinardo scoring function
add_box=2 #padding space of the ligand
Other parameters were set as default

Pose Prediction Method

Third, the most 3D similar pose (a python script was written to compute each pose's electron residue to determine the most 3D alike pose) was selected for affinity prediction.

Answer 1

No

Answer 2

Yes

1479-2-7tzaw-LigandScoringProtocol.txt

Name

NNScore

Software

Yasara/Open Drug Discovery Toolkit

Parameters

vina_gauss2, vina_repulsion, vina_hydrophobic, vina_hydrogen, vina_intra_gauss1, vina_intra_gauss2, vina_intra_repulsion, vina_intra_hydrophobic, vina_intra_hydrogen, vina_num_rotors

Method

Post docking results were first minimized using Yasara. Next, oddt was used to predict pKi by using vina features for parameters, for NNScore

Answer 1

No

Answer 2

Yes