M2ISDD_Protocol
MGLTools 1.5.6 / AutoDockTools 1.5.6 / Autodock Vina 1.1.2/ Open Babel 2.3.2 / Open-Source Pymol 1.7.x / Knime 3.4.0 + VSPrep (Gally, J. M., Bourg, S., Do, Q.-T., Aci-Sèche, S., Bonnet, P., Mol. Inf., 36, 1700023 (2017))
VSPrep Knime, babel, Scripts MGL Tools : prepare_ligands4.py
We ran our sdf file into the VSPrep workflow with knime. Then converted sdf files to mol2 files with babel and to pdbqt with MGL Tools scripts prepare_ligands4.
Autogrid4, MGLTools : prepare_dpf4
We used autogrid with the following parameters : spacing 0.208, xcenter : -5.155, ycenter : 6.527, zcenter: -3.337, 126 points for each direction.Then we used the MGLTools script : prepare_dpf4 with the default values, except for the number of poses, we ran 50 poses/Ligand. We ended by doing a general visual inspection for each pose.
We also used Autodock Vina to compare with Autodock, and we chose the best pose between the two methods for each ligand.
Yes
Yes