b6t0o-PosePredictionProtocol.txt

Name

ICM Dock

Software

Molsoft ICM 3.8-5

System Preparation Parameters

standard

System Preparation Method

Standard ICM conversion procedure was used to add hydrogens, assign atom types and charges.
Compound CatS_14 was docked to the supplied CatS_DMSO_structure_D3R_GC3.pdb with the DMSO molecule; compounds CatS_2, CatS_17, CatS_20, CatS_22, CatS_23, CatS_24 were docked to the supplied CatS_SO4_structure_D3R_GC3.pdb with the SO4 molecule. The rest of the compounds were docked to the CatS_SO4_structure_D3R_GC3.pdb without the SO4 molecule. For each pdb, two conserved water molecules (wa107 and wa134) from PDB 3MPF were added. 8 Noncovalent molecules from Pocketome entry CATS_HUMAN_114_331 (From PDB entries 3IEJ, 3KWN, 3MPF, and 3MPE) were used as Atomic Property Field bias.

Pose Prediction Parameters

Monte Carlo search 'effort' parameter was set to 10.

Pose Prediction Method

Docking runs were executed with the above specified parameters while default values
were applied for the rest of the variables. Three independent docking runs were performed and resulting poses combined.
The top 5 poses according to ICM VLS score multiplied by APF similarity to the closest template were submitted.

Answer 1

No

Answer 2

Yes