modeling zinc binding site

From: Jan Kosinski (
Date: Tue Apr 25 2006 - 07:46:30 CDT


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

Thus I need to refine the model to predict the structure of a zinc
binding site.

Is it possible to model this site using namd? Coud you propose me a
proper approach for doing this? I cannot find if someone has done
similar things. Maybe I should specify constraints for to place zinc
binding groups around zinc ion or use steered molecular dynamics?

I appreciate any help,

Jan Kosinski

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