M2ISDD_Group_A_Protocol
iCon as implemented in Ligandscout 4.2
AutoDockTools 1.5.6
Open-Source Pymol 1.8.x
AutoDock Vina 1.1.2
Scripts MGL Tools (prepare_ligands4.py)
We generate our mol2 files from a SMILES format using iCon. Then converted mol2 files to pdbqt files with MGL Tools script prepare_ligands4. pH assumed at 7.4. The protein structure used is one of the states issued from the dynamic simulation of 5QC8 named 5qc8-Cats. During the screening, receptor is defined as rigid and ligands are defined as flexible.
Iterated Local Search global optimizer search method
Exhaustiveness=8 #exhaustiveness of global search (default=8)
Vina scoring function (empirical + knowledge-based function)
center_x=-1.196
center_y=39.201
center_z=22.865
size_x=30
size_y=22
size_z=28
Num_modes=10 #max number of poses to generate
Docking runs were executed with the above specified parameters while default values were applied for the rest of the variables. Best pose from the Vina docking are submitted with this protocol.
No
Yes
M2ISDD_Group_A_Protocol
iCon as implemented in Ligandscout 4.2
AutoDockTools 1.5.6
Open-Source Pymol 1.8.x
AutoDock Vina 1.1.2
We generate our mol2 files from a SMILES format using iCon. Then converted mol2 files to pdbqt files with MGL Tools script prepare_ligands4. pH assumed at 7.4. The protein structure used is one of the states issued from the dynamic simulation of 5QC8 named 5qc8-Cats.
iCon as implemented in Ligandscout 4.2 was used to add hydrogens, and generate mol2 format of ligands. Best conformation found for each ligand was then used as a starting point for docking with Vina. Gasteiger charges were assigned to the protein and all ligands using MGLTools scripts prepare_receptor4 and prepare_ligand4 respectively. These scripts were also used to convert mol2 format into pdbqt format.
No
No