AMBER Archive (2006)

Subject: AMBER: modeling zinc binding site

From: Jan Kosinski (kosa_at_genesilico.pl)
Date: Mon Apr 24 2006 - 07:28:55 CDT

Hi,

I wish to model zinc binding site.

I have a homology model of a protein which binds zinc. The model is
based on the homolog which does not have the binding site for zinc. I
have identified potential aminoacid residues engaged in zinc binding.
However, the geometry of the zinc binding site in my homology model is
far from the geometry allowing for binding zinc -the structural elements
containing zinc binding residues must reorganize to allow for proper
geometry. Thus I need to refine the model to predict the structure of a
zinc binding site.

Coud you propose me a proper approach for doing this? I cannot find if
someone has done similar things. Maybe I should specify position
constraints for to place zinc binding groups around zinc ion?

I appreciate any help,

Jan Kosinski
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