g7q2q-LigandScoringProtocol.txt

Name

UCSF Chimera/MGLTools/AutoDock Vina/RDKIT/CDK/Knime

Software

UCSF Chimera/MGLTools/AutoDock Vina/RDKIT/CDK/Knime method 1

Parameters

Docking resolution 1
Assumed pH 7.4

Method

UCSF Chimera DockPrep script was used to add hydrogens using default parameters
and Gasteiger charges to both ligands and receptors.
Ligand conformational libraries were generated using RDKIT with Knime and tautomers with CDK.
All resulting compounds were used as starting points for Vina screening.
Preparation for docking with Vina was done using MGLTools where the ligand PDB files were converted
to PDBQTs by assigning charges and atom types. The binding site as well as the rest of the receptors
was treated as rigid and the grid box determined. Two best conformations, with regard to Vina score, were kept.

g7q2q-PosePredictionProtocol.txt

Name

UCSF Chimera/MGLTools/AutoDock Vina/RDKIT/Knime Method 1

Software

UCSF Chimera/MGLTools/AutoDock Vina/RDKIT/CDK/Knime

System Preparation Parameters

Assumed pH 7.4
Isomers considered
Tautomers considered
Gasteiger charges

System Preparation Method

UCSF Chimera DockPrep script was used to add hydrogens using default parameters
and Gasteiger charges to both ligands and receptors.
Ligand conformational libraries were generated using RDKIT with Knime and tautomers with CDK.
All resulting compounds were used as starting points for Vina screening.
Preparation for docking with Vina was done using MGLTools where the ligand PDB files were converted
to PDBQTs by assigning charges and atom types. The binding site as well as the rest of the receptors
was treated as rigid and the grid box determined.

Pose Prediction Parameters

Iterated Local Search global optimizer search method
Exhaustiveness=50 #exhaustiveness of global search (default=8)
Vina scoring funtion (empirical + knowledge-based function)
Num_modes=10 #max number of poses to generate
Energy_range=5 #energy difference (kcal/mol) between the best and worst binding mode

Pose Prediction Method

Docking runs were executed with the above specified parameters while default values
were applied for the rest of the variables. The top 2 poses from the Vina docking are submitted with this protocol.
The average value of Vina score of the two models is used for ranking compounds.