LeadFinder template docking
LeadFinder/BuildModel
Assumed pH 5
BuildModel with default parameters
Protein models were prepared using default BuildModel algorithm at pH 5. Water molecules
was retained, "normal" mode was used. Artificial template ligand was inserted into active
site during preparation. Pose obtained during cross-docking was used as a reference for
grid size calculations and template for docking for all ligands except 1, 14, 7, 9.
For ligands 1,14,7,9 part of the molecule was manually rotated around bond connecting
benzene ring and fused rings.
Template docking mode
Number of independent runs=5
LeadFinder dG scoring function (empirical function)
Docking runs were executed with the above specified parameters while default values
were applied for the rest of the variables. Poses were manually inspected and rated; poses with highest rating
from different models and runs were pooled, pose with the best dG was selected.
Yes