id-9_100x10M_sphericxraywat_adadelta_wetlig_nofilter_nobias
OpenCLAutoDock/AutoDock4.2/OpenBabel/Python/Reduce
Assumed pH 7.4, single protonation state
Gasteiger charges for both ligand and receptor
Explicit waters on ligand
Macrocycles broken
X-ray waters kept in protein
Ligand protonated at standard pH using OpenBabel based scripts.
Only one protonation state is considered. The large macrocyclic substructures of ligands
1-19 are broken to allow conformational sampling during the docking.
Protein protonated with reduce, single protonation state.
X-ray waters of the protein are modeled as spherical, i.e. they have both HB donor and acceptor
capabilities, orientation of water hydrogens is irrelevant.
Similarly, hydroxyl groups are considered disordered.
Explicit waters are added to ligand along hydrogen bond vectors.
100 Genetic Algorithm (GA) instances
10 million energy evals per GA
Local search frequency: 100 percent
Local search max evals: 500
Local search method: Adadelta
Macrocyclic ligands are docked in an open conformation and
a linear potential is used to bring the broken bond back together (50 kcal/mol/angstrom).
The ranking of the poses is provided by the AutoDock4.2 scoring function.
No
No