1146-1-8x0mu-PosePredictionProtocol.txt

Name

Knime/RDKIT/Chemaxon/MGLTools/Autodock Vina

Software

Knime/RDKIT/Chemaxon/MGLTools/Autodock Vina

System Preparation Parameters

Assumed pH 7.0
Tautomers considered
Chemaxon majormicrospecies

System Preparation Method

Knime was used to read the Smiles, we generated the coordinates throught the RDKIT node and 50 conformers of each ligand. Each conformer was protonated with Chemaxon at pH 7.0 using the majormicrospecies method. We used MGLTools to transform mol2 files to pdbqt files for screening with AutoDock Vina.

Pose Prediction Parameters

Iterated Local Search global optimizer search method
Exhaustiveness=8 #exhaustiveness of global search (default=8)
AutoDock41 scoring funtion
Num_modes=20 #max number of poses to generate
Energy_range=5 #energy difference (kcal/mol) between the best and worst binding mode

Pose Prediction Method

Screening was made with AutoDock Vina, with the parameters above then we applied the AutoDock41 scoring function.

Answer 1

No

Answer 2

Yes