Name

M2ISDD_3IEJ

Software

Autodock 1.5.6/iCon/MGLTools 1.5.6/AutoDock Vina 1.1.2

System Preparation Parameters

prepare_ligands4.py of MGLTools

System Preparation Method

iCon generated sdf files were converted to mol2 with babel and to pdbqt with babel

Pose Prediction Parameters

Grid generated with following parameters. center_x=37.489,center_y=34.681,center_z=40.326,size_x=28,size_y=28,size_z=28,num_modes = 10,exhaustiveness = 8

Pose Prediction Method

We used Autodock Vina on a box centered on the active site.

Answer 1

No

Answer 2

Yes

Name

M2ISDD_3IEJ

Software

AutoDock Vina 1.5.6/iCon 4.2

Parameters

Docking resolution 2
Assumed pH 7.4

Method

We used iCon to create conformations and to protonate our ligands using defaut parameters and an assumed pH of 7.4. The binding site residues, which were considered to be residues. The most stable conformation found for each ligand was then used as a starting point for docking with Vina. We used prepare_ligand4.py from Autodock to add hydrogens and convert ligands in mol2 to pdbqt.

Answer 1

No

Answer 2

No