ICM Dock
Molsoft ICM 3.8-7b
standard
Standard ICM conversion procedure was used to add hydrogens, assign atom types and charges.
All compounds were docked to an ensemble of 2 PDBs (5QBU and 5QC6)
24 co-crystallized ligands from 13 PDBs (3IEJ, 5QBU, 5QBX, 5QC1, 5QC3, 5QC4, 5QC5, 5QC6, 5QC8, 5QCA, 5QCD, 5QCE, 5QCJ)
were used as Atomic Property Field bias.
For each of the 2 PDB used, a docking energy offset was generated by redocking 24 co-crystallized molecules, optimizing the ligand and receptor Calpha RMSD
Monte Carlo search 'effort' parameter was set to 10.
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.
A composite score of ICM VLS score and APF similarity to the closest template were calculated
All poses with composite score better than 0 were kept.
430 Compounds from ChEMBL_24 and D3R 2017 were docked using the same procedure.
A pose selection procedure is conducted in which an initial 3D-QSAR model was trained to predict the compound's pKd value,
the model is applied to all poses kept, the pose producing the higest predicted pKd value was selected to build the next 3D-QSAR model
This procedure was repeated for 10 rounds to select final poses and generate the final 3D-QSAR model.
The final 3D-QSAR model was then applied to the challenge compounds' available poses, the pose generating the highest predicted pKd value is kept
The predicted pKd value is converted into Binding Energy.
No
Yes
ICM Dock - iterative APF 3D QSAR
Molsoft ICM 3.8-7b
Monte Carlo search 'effort' parameter was set to 10.
Standard ICM conversion procedure was used to add hydrogens, assign atom types and charges.
All compounds were docked to an ensemble of 2 PDBs (5QBU and 5QC6)
24 co-crystallized ligands from 13 PDBs (3IEJ, 5QBU, 5QBX, 5QC1, 5QC3, 5QC4, 5QC5, 5QC6, 5QC8, 5QCA, 5QCD, 5QCE, 5QCJ)
were used as Atomic Property Field bias.
For each of the 2 PDB used, a docking energy offset was generated by redocking 24 co-crystallized molecules, optimizing the ligand and receptor Calpha RMSD
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.
A composite score of ICM VLS score and APF similarity to the closest template were calculated
All poses with composite score better than 0 were kept.
430 Compounds from ChEMBL_24 and D3R 2017 were docked using the same procedure.
A pose selection procedure is conducted in which an initial 3D-QSAR model was trained to predict the compound's pKd value,
the model is applied to all poses kept, the pose producing the higest predicted pKd value was selected to build the next 3D-QSAR model
This procedure was repeated for 10 rounds to select final poses and generate the final 3D-QSAR model.
The final 3D-QSAR model was then applied to the challenge compounds' available poses, the pose generating the highest predicted pKd value is kept
The predicted pKd value is converted into Binding Energy.
No
Yes