id-10_100x10M_noxraywat_adadelta_drylig_nofilter_nobias
OpenCLAutoDock/AutoDock4.2/OpenBabel/Python/Reduce
Assumed pH 7.4, single protonation state
Gasteiger charges for both ligand and receptor
Macrocycles broken
6-member ring in ligand BACE_13 modeled as two rigid conformations
X-ray waters removed from 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.
Hydroxyl groups are considered disordered.
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.
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