I have doubts whether to remove the water molecules from the pdb before docking, since, when checking the molecule by autodock tools, I get an alert that all the molecules that are not attached to the protein, in this case the water and ions. But I also understand that these water molecules may or may not favor docking. Help :c
Usually we remove the water molecules along with other ions in the protein structure (Just keep only the desired protein chain of interest for docking protocol). Or else this will unnecessarily interact with the ligand and give false results.
Regards.
Yes water molecules should be removed from the protein before docking, by autodock, or any docking software.
But sometimes its is require for some protein-ligand docking, just go through literatures for your interested protein.
You should remove all the HETATM i.e. non-protein components prior to docking. Only if a water molecule is known to bind along with ligand or consensus water is present with the ligand, binding to the active site for a family of proteins, you may need to preserve it. But do remember, that is what you do in hydrated docking approach in autodock not the normal protocol of autodock.
Dear reseachers
I think you see if the native ligand forms interactions with water or no. if it establish H bond with water molecules you must keep them
Best regards
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