AutoDockVina
AutoDock Vina 1.1.2
Assumed pH 7.4
Tautomers considered only for BACE_5
Ligand protonation state was generated at pH 4.5 using pKa Plugin from ChemAxon. Pdb4amber was used to renumber the protein residues in the PDB structures with only positive integer residue numbers. Pdbfixer was used to remove the ligand and the water molecules and to add the missing heavy atoms to the pdb structures of the receptors. Then, PDB2PQR server (http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/) was used to correct the protonation states at pH 4.5 and to fix the residue/atom names following AMBER naming scheme. Parmed was used to convert the resulting pqr file to a pdb file. OpenEye toolkits were used to check bond-order and connectivities. Lastly scripts in MGLTools (v 1.10) were used to prepare pdbqt files for AutoDock Vina.
exhaustiveness = 50
num_modes = 50
energy_range = 5
We have used the 20 BACE structures provided by the D3R Challenge to dock the ligands. The docked poses from AutoDock Vina were visually inspected and compared to the most similar reference ligand(s) from the PDB database. The closest pose to the reference ligand was then selected.
Yes
Yes