ICM/APF 3D QSAR
Molsoft ICM 3.8-7
default
CatS ligands with Tanimoto similarity > 0.6 to the challenge ligands were extracted from ChEMBL v. 2.3. 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. Predicted value was converted to binding energy in kcal/mol.
no
ICM Dock
Molsoft ICM 3.8-7
standard
Standard ICM conversion procedure was used to add hydrogens, assign atom types and charges.
4 receptor structures were selected from a pool of PDBs combining the pocketome entry and the structures released in Stage 1b, based on their ability to re-dock the co-crystallized ligands correctly.
Monte Carlo search 'effort' parameter was set to 20.
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.
For each ligand, the best pose was selected by the sum of normalized ICM VLS score and normalized APF similarity to co-crystallized ligands.
No
Yes