After removing the inhibitor from the protein and then preparing it for docking, how can I be sure whether the ligand of my interest is attached to the most active site.
1) Dock the ligand onto your protein ( I assume you are talking about blind docking). You will get several different docking poses that are energetically ranked from best pose to least best.
2) Look for the holo structure of your protein or one of its homologues co-crystallized with substrate analogue in PDB. OR extract the active site information from catalytic site atlas.
3) Superpose your structure, along with the docked ligand, with the holo structure. If the substrate analogue overlaps with your docked ligand, you are sure that the ligand has gone and docked itself into the active site ( However, this in no way validates the docked pose as being true; it just tells that the ligand is docked in the active site) OR if you obtain the active-site residues predicted by catalytic site atlas within 4 A of the docked ligand, your ligand has hit the active site.
I hope the answer helps.
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