AutoDock 4.x GPU with substructure filters
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.
Every pose is subjected to post-processing filters to evaluate similarity with known
binding modes. The following smarts strings and associated reference ligands were
considered:
4dpf, [CX4][CX4]([OH1])[CX4][NX3][CX3]=O
2f3f, [CX4][NX3][CX3](=[O])[CX4]([CX4])[CX4][CX4]([OH1])[CX4][NX3][CX3]=O
4dpf, [CX4][N][CX4][CX4]([OH1])[CX4][NX3][CX3]=O
4dpf, [CX4][c][c][c][CX4][N][CX4][CX4]([OH1])[CX4][NX3][CX3]=O
4dpf, [CX4]([OH1])[CX4][NX3][CX3](=O)[a]1[a][a][a][a][a]1
2f3f, [CX4]([OH1])[CX4][NX3][CX3](=O)[CX4][NX3][CX3](=[O])[CX4]
4k8s, [CX4]([OH1])[CX4]([CX4][a]1[a][a][a][a][a]1)[NX3][CX3](=O)
All poses passing similarity filters are submitted for evaluation.
The ranking of the poses is provided by the AutoDock4.2 scoring function.
Ligand BACE_3 was chery picked because not a single pose passed the automated filters.
No
Yes