1146-1-72jhm-PosePredictionProtocol.txt

Name

DockQ

Software

MOE2016.08/Autodock4/MGLTools1.5.7RC1/AMBER16/LigPrep/RDKit2018-3

System Preparation Parameters

6BFE was used as the receptor. It was protonated with MOE and checked manually.

System Preparation Method

Ligands were prepared with LigPrep and manually curated to check for correct ligand conformations.
Receptor and Ligands were converted to pdbqt using MGLTools.
In house scripts were used to introduce aromatic and polar biases (Hydrogen Bond donor and Receptor) into docking runs.
(Arcon, JP; et al, JCIM 2017)

Pose Prediction Parameters

-Mixed CoSolvent MD (20ns x3) in Ethanol and Water. Parameters can be found in Arcon, JP, et al, 2017 JCIM.
Standard Autodock paramters were used except:
ga_runs 100
energy_eval = 1000000
Biases were applied to ligands with aromatic rings placing a dummy atom at the center of mass of the rings.

Pose Prediction Method

Molecular Dynamics in Mixed solvents (Ethanol and Phenol) to determine Solvent Sites.
Standard Docking run with Autodock with biases.

Answer 1

Yes

Answer 2

Yes