I have prepared a protein in 2 ways, one in which I kept only constraint co-crystalized water molecules i.e. crystalized ligand bind with those water molecules and deleted all other water molecules.
In a 2nd way, I kept water molecules 6A distant from ligand and deleted others. I docked some ligands and calculate binding energy (dG), but they give a huge binding energy difference with these two way of proteins. So, I'm confused which one I should take in account? Which one is correct?
Crystallization water presence or abscence depends on literature some H- bond key interactions take place via water molecules if this the case with your protein leave only those involved if not delete all water.
You can consider the first one - where you have kept water molecules present in the binding site that is also involved in the interaction.
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