mbbz2-LigandScoringProtocol.txt

Name

Vina-Smina method 2

Software

molconverter/Obabel/AutoDock Vina-Smina

Parameters

exhaustiveness 12
Assumed pH 7.4

Method

We used obabel to add hydrogens and to convert smiles to 2D sdf
and molconverter (ChemAxon) to compute 3D coordinates using default parameters
and assume pH of 7.4. pdb structures for docking were selected based on similarity
of current ligand to co-cristallized (tanimoto indexes were computed with obabel)
Docking was performed via Vina-Smina programm with vinardo scoring functions.

mbbz2-PosePredictionProtocol.txt

Name

Vina-Smina method

Software

molconverter/Obabel/MGLTools/AutoDock Vina-Smina

System Preparation Parameters

Assumed pH 7.4
Tautomers considered
Gasteiger charges

System Preparation Method

All the waters and ligands were removed from the model.
Preparation for docking with Vina-Smina was done using MGLTools where the PDB files
were converted to PDBQTs by assigning charges and atom types.

Pose Prediction Parameters

Iterated Local Search global optimizer search method
Exhaustiveness=12 #exhaustiveness of global search (default=8)
scoring funtions : vinardo
Num_modes=1 #max number of poses to generate

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 1 poses from the Vina-Smina docking were used.