id-11_100x10M_sphericxraywat_adadelta_drylig_nofilter_yesbias
OpenCLAutoDock/AutoDock4.2/OpenBabel/Python/Reduce
Assumed pH 7.4, single protonation state
Gasteiger charges for both ligand
Macrocycles broken
6-member ring in ligand BACE_13 modeled as two rigid conformations
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.
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 scoring function is biased to penalize docking poses that differ from the x-ray
coordinates of ligand 4dpf, with respect to atoms O15, N16 and C18.
The penalty is applied if the corresponding BACE ligand atoms are at a distances
larger than 1.2 angstroms from the corresponding reference atom (either O15, N16 or C18 in 4dpf).
The ranking of the poses is provided by the AutoDock4.2 scoring function.
No
Yes