1146-1-p5fhu-PosePredictionProtocol_GPU_no-filters.txt

Name

AutoDock 4.x GPU

Software

AutoDock4.x GPU/OpenBabel/Python

System Preparation Parameters

Assumed pH 7.4
Gasteiger charges

System Preparation Method

Ligand protonated at standard pH
Only one protonation state is considered.
Protein protonated with reduce.

Pose Prediction Parameters

between 2 - 10 million evaluation per docking run
300 - 400 docking runs

Pose Prediction Method

Macrocyclic ligands are docked in an open conformation.
A linear potential is used to bring the broken bond back together.
The ranking of the poses is provided by the AutoDock4.2 scoring function.

Answer 1

No

Answer 2

No