Pose prediction
Maestro/Ligprep/Prep wizard/Glide
Assumed pH 5-7
Tautomers considered
OPLS2005
Maestro's prepwizard was used to add hydrogens using default parameters.
All the waters were removed while OPLS2005 force field parameters were assigned to the protein and all
ligands. The binding site residues, which were considered to be residues 56, 65, 200 and 210, were energy minimized.
Ligand conformational libraries were generated using Ligprep.
Glide xp was used for docking
Scaling factor: 0.8 Partial charge cutoff: 0.15
Sample nitrogen inversions
Add Epik state penalties to docking score
Preform post-docking minimization
Sample ring conformation
Docking runs were executed with the above specified parameters while default values
were applied for the rest of the variables. Only one pose was output for each ligand