pf7ru-LigandScoringProtocol.txt

Name

M2ISDD_Protocol

Software

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

Parameters

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.

Method

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.

Answer 1

No

pf7ru-PosePredictionProtocol.txt

Name

M2ISDD_Protocol

Software

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))

System Preparation Parameters

VSPrep Knime, babel, Scripts MGL Tools : prepare_ligands4.py

System Preparation Method

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.

Pose Prediction Parameters

Autogrid4, MGLTools : prepare_dpf4

Pose Prediction Method

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.

Answer 1

Yes

Answer 2

Yes