VINA_VINA
iCon/ChemAxon/MGLTools/AutoDock Vina
Assumed pH 7.4
All iCon conformers considered (50 per ligand)
Gasteiger charges
Proteins were protonated at pH 7.4 using pdb2pqr that calls ProPKA. Amber force field parameters were assigned to the protein.
Ligand conformational libraries were generated using iCon as implemented in LigandScout 4.2.
All ligands were protonated at pH 7.4 using ChemAxon and considereing the major microspecie only.
All protonated conformations generated for each ligand were then used as a starting point for docking.
Preparation for docking with Vina was done using MGLTools where the ligand SDF files were converted to PDBQTs by assigning charges and atom types.
Iterated Local Search global optimizer search method
Exhaustiveness = 8
num_modes = 20
Scoring funtion = Vina (empiric + knowledge based)
Docking runs were executed with the above specified parameters while default values
were applied for the rest of the variables. Top one pose according to VINA scoring function ranking was considered for each ligand.
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