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Ligand Energy in 2 two receptors..

PostPosted: Tue Jun 28, 2016 10:21 am
by sgaray
Hi everyone

I have docked the same ligand in the same protein but in one case I did it with the natural ligand in its pocket and in the other case without it. The idea was to check if the ligand was able to join to the receptor interacting with the natural ligand too. So, my question I think is rather conceptual:

Can I compare the Energy/Score of the Ligand docked in these both situations?
As I see, the energy coming from (Protein1_Ligand_Joined - Protein1_Ligand_NO_Joined) it would be different from (Protein2_Ligand_Joined - Protein2_Ligand_NO_Joined) and in this way It would not be comparable.

Thank you for your help