1470-1-xf0i5-id-4_200x32M_sphericxraywat_soliswets_drylig_nofilter_nobias.txt

Name

id-4_200x32M_sphericxraywat_soliswets_drylig_nofilter_nobias

Software

OpenCLAutoDock/AutoDock4.2/OpenBabel/Python/Reduce

System Preparation Parameters

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

System Preparation Method

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.

Pose Prediction Parameters

200 Genetic Algorithm (GA) instances
32 million energy evals per GA
Local search frequency: 100 percent
Local search max evals: 500
Local search method: Solis-Wets

Pose Prediction Method

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.

Answer 1

No

Answer 2

No