1146-1-0ymfy-PosePredictionprotocol.txt

Name

VINA_ADT

Software

iCon/ChemAxon/MGLTools/AutoDock Vina/AutoDock 4.2

System Preparation Parameters

Assumed pH 7.4
All iCon conformers considered
Gasteiger charges

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.
Preparation for docking with Vina was done using MGLTools where the ligand SDF files were converted to PDBQTs by assigning charges and atom types.

Pose Prediction Parameters

Iterated Local Search global optimizer search method
Exhaustiveness = 8
num_modes = 20
Scoring funtion = AutoDock4.2

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 AutoDock 4.2 scoring function with the default parameters. Only Top 1 poses were retained for submission.

Answer 1

No

Answer 2

No