[Protein-analysis] Re: inorganic mol. docking

Clement Angkawidjaja via proteins%40net.bio.net (by clement from bio.mls.eng.osaka-u.ac.jp)
Mon May 19 18:59:54 EST 2008

Do you want to dock with density data or prediction?

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

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.


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Subject: Proteins Digest, Vol 36, Issue 5

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> Date: Sun, 18 May 2008 09:23:51 -0700 (PDT)
> From: sudha.mrig from gmail.com
> Subject: [Protein-analysis] inorganic mol. docking
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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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