AutoDock 4.x GPU with visual inspection
AutoDock 4.x GPU
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.
For every ligand, docking poses have been clustered and visually inspected to
select poses bining similarly to ligand conformations determined by crystallography
A single pose is submitted per ligand
Yes
No