Hello RG Community I hope your well:),

towards the above topic, I have generated 10 ligand 3-D Conformational Structures via a SMILES within PubChem, there are no PDB Images yet for this ligand-protein complex. My Aim is to dock this ligand to the protein, where each docking would generate 9-models ultimately generating 90-docked models in total.

All of the SDF Downloaded Coordinates of the 10 ligands exhibit similar energies and subsequent to visualizing 9-models generated via the first ligand docking, all models exhibited similar docking energies, similar amounts of hydrogen bonds and other bonds and similar visuals.

To manage time is there a way to critically select one of the conformations amongst the others nine?

Similarly is there a critical way to choose one of the models generated amongst the remaining 8 models generated?

(I think in this case due to the lack of experimental evidence, this would be trial and error based.)

And I have elected the PubChem over other website Smiles to 3-D Conformational generators due to their more in depth algorithms, would you agree that PubChem would be amongst the top-rated 3-D conformational generators?

Thanks if you have any suggestions:),

Joel 🚀