1146-1-g3x7c-PosePredictionProtocol.txt

Name

ICM Dock with 4D receptor ensemble and APF ligand bias

Software

Molsoft ICM 3.8-7b

System Preparation Parameters

standard

System Preparation Method

Standard ICM conversion procedure was used to add hydrogens, assign atom types and charges.
All compounds were docked to an ensemble of 7 PDBs (2F3E, 2F3F, 3K5C, 3K5D, 4DPI, 4GMI, 4PDF)
For each PDB, two alternative protonation states were generated in which either Asp 80 or Asp 276 was protonated.
14 molecules from PDBs (2F3E, 2F3F, 3DUY, 3DV1, 3DV5, 3K5C, 3K5D, 3K5G, 4DPF, 4DPI, 4GMI, 4K8S, 4KE0, 4KE1) were used as Atomic Property Field bias.
For each PDB in the receptor ensemble, a docking energy offset was derived by redocking 14 co-crystallized molecules, optimizing the ligand and receptor Calpha RMSD

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 the sum of normalized ICM VLS score and APF similarity to the closest template were submitted.

Answer 1

No

Answer 2

Yes