inorganic mol. docking

Do you want to dock with density data or prediction?

If you have density, recent versions of COOT can do that without much
hassle.

If you do simulation, most docking softwares can do that. My favourite is
Autodock. it's free for academics. Just generate your ligand as a pdb and
follow the online instruction.

Most metal ions are present as single ion species. It is very very difficult
to precisely predict the binding sites of ions in a protein except for the
known motifs (active sites, metal-binding motifs such as Zn finger,
beta-roll, etc). These kinds of ion are usually present in the protein
structure. no docking needed.

Clement

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Sent: Tuesday, May 20, 2008 2:03 AM
Subject: Proteins Digest, Vol 36, Issue 5