What to do after protein-ligand docking? Is there any necessary or enhancement step recommended after docking to validate the confirmation of highest score is the best? For your information, I am using CCDC GOLD for docking and GOLD score as my scoring function.
You can run a Molecular Dynamics simulation to see if the pose is stable and whether the protein changes/adapts it’s conformation.
You can calculate the ligand efficiency, the docking score divided by the number if heavy atoms, and rank the compounds accordingly.
You can also compare the scores of known ligands to the experimental values and see if the docking the scores are predicting known ligands or correlate with the experimental ones.
At some point you have to make a selection and purchase or synthesize the compounds. How many compounds can you test experimentally? How many can you purchase? What is the purpose of these ligands going to be? Drugs? Did you screen the correct set of ligands e.g. a library of lead compounds that are ready to purchase for cheap, that would be a good start.