Champion's_List
iCon/ChemAxon/rDock/VINA/SeeSAR/AutoDOck 4.2/rDock_solv
Assumed pH 7.4
All iCon conformers considered
No partial charges considered using rDock
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.
No partial charges are considered using rDock.
Preparation for docking with Vina was done using MGLTools where the ligand SDF files were converted to PDBQTs by assigning charges and atom types.
VINA Iterated Local Search global optimizer search method
VINA Exhaustiveness = 8
VINA num_modes = 20
rDock num_modes = 50
Scoring funtion = VINA/rDock/rDock_solv/AutoDock4.2/SeeSAR
Docking runs were executed with the above specified parameters while default values
were applied for the rest of the variables. Generated poses were scored using VINA, rDock, rDock_solv, AutoDock4.2, SeeSAR scoring function with the default parameters.
Top 1 pose for each score and for each molecules were considered. On the basis of visual inspection, only one pose per molecule was retained for submission.
Yes
Yes