AutoDock 4.x GPU
AutoDock4.x GPU/OpenBabel/Python
Assumed pH 7.4
Gasteiger charges
Ligand protonated at standard pH
Only one protonation state is considered.
Protein protonated with reduce.
between 2 - 10 million evaluation per docking run
300 - 400 docking runs
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.
No
No
AutoDock-GPU / Substructure filters
AutoDock-GPU / AutoDock4.2 / OpenBabel
Mostly default
raw docking results were re-ranked using a common pharmacophore model built using about 350 ligand
structures co-crystallized in the PDB.
Results have been ranked by their pharmacophore score (i.e. how the model was matched).
No
No