M2ISDD_Protocol
MGLTools 1.5.6 / AutoDockTools 1.5.6 / 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)) / Autodock Vina 1.1.2
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 script prepare_ligands4. pH assumed at 7.4. The structure used as a protein is the CatS_SO4_structure_D3R_GC3 without the SO4.
Obabel was used to add hydrogen to a 7.4 pH, gasteiger charges were added. We used Vina then to obtain an energy score once our pdbqt files were ready.
No
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