1146-1-kgq4m-PosePredictionprotocol.txt

Name

rDock_rDock

Software

iCon/ChemAxon/rDock

System Preparation Parameters

Assumed pH 7.4
All iCon conformers considered
No partial charges considered using rDock

System Preparation Method

Proteins were protonated at pH 7.4 using pdb2pqr that calls ProPKA. Amber force field parameters were assigned to the protein.
Ligand conformational libraries were generated using iCon as implemented in LigandScout 4.2.
All ligands were protonated at pH 7.4 using ChemAxon and considereing the major microspecie only.
All protonated conformations generated for each ligand were then used as a starting point for docking.
No partial charges are considered using rDock.

Pose Prediction Parameters

num_modes = 50

Pose Prediction Method

Docking runs were executed with the above specified parameters while default values
were applied for the rest of the variables. Generated poses were scored using the rDock scoring function with the default parameters. Only Top 1 poses were retained for submission.

Answer 1

No

Answer 2

No