How to differentiate among the mode of binding of ligands in different proteins having same set of identical or similar active site residues?

11 November 2013 1 6K Report

I am doing docking studies on some proteins belonging to same protein family but different organism, but don't know how to differentiate out the difference in binding mode of ligands to the binding site.

Rajeev Ranjan Roy

Hi Deepka,

Thanks for your reply.

yes, you are right, in terms of docking studies based on geometry or spatial arrangement of the binding pocket formed by the active site residues but I want to differentiate the binding mode of different ligands on the basis of the chemical properties of the binding pocket.

If you have any idea regarding this, please help me with your valuable suggestion.

I am waiting for your response.

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