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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Subject: Proteins Digest, Vol 36, Issue 5
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>>> Today's Topics:
>> 1. inorganic mol. docking (sudha.mrig from gmail.com)
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>> Message: 1
> Date: Sun, 18 May 2008 09:23:51 -0700 (PDT)
> From: sudha.mrig from gmail.com> Subject: [Protein-analysis] inorganic mol. docking
> To: proteins from net.bio.net> Message-ID:
> <a40b53bb-1b35-4399-ba18-b5fbb89e4830 from j33g2000pri.googlegroups.com>
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>> I want to dock an inorganic molecule like ZnSO4, MgOAc etc. with a
> protein molecule. I could not locate any docking software which can
> handle in organic molecule. If anyone can help me in this regard.
> Thanks
>> Sudha
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