Name

ICM/APF 3D QSAR

Software

Molsoft ICM 3.8-5

Parameters

default

Method

302 CatS ligands were obtained from ChEMBL. They were docked and their best docking pose selected using the same procedure as for challange ligands. Best scoring docking poses for all ChEMBL compounds were used to train a APF-3D-QSAR model to predict its pKd. The resultant model was used to predict the the pKd of the 136 ligands in the challenge. The predicted pKd value is used as the final score of the compound.

Answer 1

no

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.
All 136 ligands were docked to the supplied CatS_DMSO_structure_D3R_GC3.pdb with the SO4 molecule removed. Two conserved water molecules (wa107 and wa134) from PDB 3MPF were added. PDB entries 3IEJ, 3KWN, 3MPF, and 3MPE were used as templates for 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 1 pose according to ICM VLS score multiplied by APF similarity to the closest template were submitted.

Answer 1

No

Answer 2

Yes