1146-1-gcyge-PosePredictionProtocol.txt

Name

2vinardo-beta

Software

rdkit / MGLTools/ smina (modified)

System Preparation Parameters

Assumed pH 4.5 (protonated ASP, GLU )
Tautomers not considered
rdkit used to generate a maximum of 20 conformers per ligand using ETKDG method.

System Preparation Method

prepare_receptor4.py script from MGLTools, which removes water molecules, was used on pdb code 3DUY.
Charged aminoacids and ligands were modified acording to our new parameter scheme in 2vinardo.
Ligands structures were generated with RDKIT from the provided smiles. A total of 20 conformers for each ligand were generated..
Inputs for docking (pdbqt files) were generated with prepare_ligand4.py from MGLTools.
Binding site was kept rigid.

Pose Prediction Parameters

Exhaustiveness=64 #exhaustiveness of global search (default=32)
2Vinardo (beta) scoring function (modification of Vinardo, which is based on Autodock Vina)
Num_modes=1 #max number of poses to generate

Pose Prediction Method

Docking runs were executed with the above specified parameters while default values
were applied for the rest of the variables. We used the crystal structure of the 3DUY PDB entry, which consists of co-cristalizaed BACE and
(2R,4S,5S)-N-butyl-4-hydroxy-2,7-dimethyl-5-{[N-(4-methylpentanoyl)-L-methionyl]amino}octanamide. The top 5 poses according to the scoring
function, after analyzing only the top pose for each of the 20 conformers for each Ligand are submitted with this protocol.

Answer 1

No

Answer 2

No

1146-2-x5xbv-LigandScoringProtocol.txt

Name

2vinardo-beta

Software

rdkit / MGLTools/ smina (modified)

Parameters

Assumed pH 4.5 (protonated ASP, GLU )
Tautomers not considered
rdkit used to generate a maximum of 20 conformers per ligand using ETKDG method.

Method

System Preparation Method: prepare_receptor4.py script from MGLTools, which removes water molecules, was used on pdb code 3DUY.
Charged aminoacids and ligands were modified acording to our new parameter scheme in 2vinardo.
Ligands structures were generated with RDKIT from the provided smiles. A total of 20 conformers for each ligand were generated..
Inputs for docking (pdbqt files) were generated with prepare_ligand4.py from MGLTools.
Binding site was kept rigid.

Pose Prediction Method

Docking runs were executed with the above specified parameters while default values
were applied for the rest of the variables. We used the crystal structure of the 3DUY PDB entry, which consists of co-cristalizaed BACE and
(2R,4S,5S)-N-butyl-4-hydroxy-2,7-dimethyl-5-{[N-(4-methylpentanoyl)-L-methionyl]amino}octanamide. The top 5 poses according to the scoring
function, after analyzing only the top pose for each of the 20 conformers for each Ligand are submitted with this protocol.

Answer 1

No

Answer 2

No