fznsu-PosePredictionProtocol.txt

Name

Vina

Software

AutoDock Vina 1.0

System Preparation Parameters

Gasteiger charges #Vina

System Preparation Method

Waters/cofactors were removed
from the bound protein structures. Then a cleaned bound protein
structures was used for docking.
Preparation for docking with Vina was done using MGLTools.

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

A query ligand was docked to the cleaned bound protein structure using
Vina. Top 5 models were selected for D3R submission.

Answer 1

No

Answer 2

Yes