What should I look for when I visualize a docked compound?Up to table of contents
This FAQ applies to: AutoDock 3, AutoDock 4
The first thing to check is that the ligand fits into some kind of pocket on the receptor. The second is that there is a chemical match between the atoms in the ligand and those in the receptor. For example, check that carbon atoms in the ligand are near hydrophobic atoms in the receptor, while nitrogens and oxygens in the ligand are near complementary hydrogen bonding atoms. Check for charge complementarity. Also consider whatever else you may know about your particular system: for instance, if you know the mechanism of action of the enzyme and which residues are involved, examine how the ligand binds to these residues. In the case of HIV-1 Protease, good inhibitors bind in a mode that mimics the transition state, placing a hydroxyl group near the two catalytic aspartic acid sidechains.