1479-1-rjj3c-PosePredictionProtocol.txt

Name

VINA_rDock_solv

Software

iCon/ChemAxon/MGLTools/AutoDock Vina/rDock

System Preparation Parameters

Assumed pH 7.4
All iCon conformers considered (50 per ligand)
Gasteiger charges

System Preparation Method

Proteins were protonated at pH 7.4 using pdb2pqr that calls ProPKA. For each ligand, the structure of BACE co-crystallized with the most similar ligand in terms of volume and physico-chemical properties (visual inspection) was selected for docking. 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 = Vina (empiric + knowledge based)

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 a consideration of the solvation potential. Only Top 1 poses was considered for each ligand.

Answer 1

No

Answer 2

No

1479-2-wsafc-LigandScoringProtocol.txt

Name

VINA_rDock_solv

Software

iCon/ChemAxon/MGLTools/AutoDock Vina/rDock_solv

Parameters

Assumed pH 7.4
All iCon conformers considered
Gasteiger charges

Method

Proteins were protonated at pH 7.4 using pdb2pqr that calls ProPKA. For each ligand, the structure of BACE co-crystallized with the most similar ligand in terms of volume and physico-chemical properties (visual inspection) was selected for docking. 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 = rDock_solv (empirical function)

Answer 1

No

Answer 2

No