Iam working with a Zn metalloprotein. I’ve finished some docking on a zinc-containing protein using AutoDock Zn. I need to take only 1 docking (best one) to visualise using discovery studio and rest all docking for results and interpretation.
I chose docking result of one protein-ligand pair (one with lowest binding energy from the whole data - for visualisation). From the RMSD table of that, “run 3” (pose 3) has the lowest binding energy, so at first I planned to use that as my “best pose” for visualization and analysis. But when I loaded it in PyMOL, the ligand in pose 3 is quite far from the catalytic Zn and doesn’t seem to interact with it at all.
In the same docking output, another pose (pose 10) places the ligand much closer to the zinc and looks more like a realistic metal-binding orientation, but its binding energy is not the lowest.
My situation is:
- I have close to 200 docking runs in total for results, interpretation etc..
- For the write-up and figures, I mainly need to visualize one representative complex.
- For this particular ligand, pose 3 has the best (most negative) binding energy but poor Zn proximity.
- Pose 10 has a slightly worse energy but is the only one that sits properly near Zn.
For my results, graphs, and text, can I:
- Use the binding affinity value from pose 3 (lowest energy),
- But use pose 10 only for visualization,
or is that considered methodologically wrong because the energy and the visualized pose would come from different docking solutions?
For data analysis (results, interpretation, graphs etc), can I use the lowest docking energy for each protein–ligand pair, because it is not practical to visually inspect every pose for all compounds.
