How could we do protein docking study for co crystal molecules?

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Temidayo Osadipe

Sankara Narayanan , what to do is to split the protein you retrieved from PDB into protein, ligand and water( as you know that deposited protein consist of the protein, co-crystalized ligand and molecules of water) after which, you dock the co-ligand into the grid generated to get your docking score.

Samuel Olawale Olubode

I agree with Temidayo Osadipe's answer. You can as well get information about the co-crystalized compound's name and download the structure online or you draw the structure.

Sankara Narayanan

Thank You for your suggestion @Osadipe and Samuel