Subject: docking ligand to mutant protein

From: "[email-masked]" <[email-masked]>
Date: Thu, 17 Oct 2002 11:52:14 -0400

Dear All,

When using Autodock3.0 to dock a ligand to a mutant protein, the
estimated free energy of binding and also hydrogen bonds detected
indicate that the ligand will bind to the mutant but experimental work
has shown that it does not. I have used the same procedure to dock the
same ligand to the wild-type protein and the result was consistent with
experimental results. My mutant protein was prepared from the wild-type
crystal structure (changed the residues using insightII).

I'd like to ask whether anyone has encountered such a problem before.
Could it be that the mutant protein structure was not suitable? An idea
was proposed that the overall charge of the mutant and wild-type protein
should remain the same, therefore, if the net charge for the mutant is
less, then some residues should be mutated in order to obtain the same
net charge as the wild-type protein.

I'd appreciate any suggestions/feedback.

Thank you all for your time.

Kind regards,
Rowyna

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