dbtcn-PosePredictionProtocol.txt

Name

Vina_wat

Software

AutoDock Vina 1.0

System Preparation Parameters

Gasteiger charges #Vina

System Preparation Method

Waters/cofactors in the bound protein structures were
kept 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 bound protein structure using
Vina. Waters/cofactors were considered in the dokcing process.
Top 5 models were selected for D3R submission.

Answer 1

No

Answer 2

Yes