[BiO BB] Generate Quaternary structure of protein from monomer

Dr.Nagasuma Chandra nchandra at physics.iisc.ernet.in
Fri Mar 4 01:07:47 EST 2005

Hi Subhash

  First of all, you need to be sure that your model will have the same 
quaternary arrangement as your template. There are a number of examples, 
where diversity is observed in  quaternary structure even when subunit 
structures (and their sequences) show high similarity (>50-70%). Plant 
lectins are a classic example. If you are sure of the type of quaternary 
association, either from biochemical data and/or  structural analysis of 
your model and its comparison to the template, it is relatively simple to 
apply the translational and rotational matrices to obtain a multimer.

Hope this helps
Nagasuma Chandra
   Dr. Nagasuma Chandra
   Bioinformatics centre
   Indian Institute of Science
   Bangalore 560 012
   Tel: +91-80-22932469 or 23601409
   Fax: +91-80-23600551 
   e-mail: nchandra at physics.iisc.ernet.in

On Fri, 4 Mar 2005, Subhash Agarwal wrote:

> Hi all
> Reply to Dan Bosler answer
> I knew of these sites and visited them again after u
> referred. These sites are useful if u have a pdb code
> avaliable. In my case i have built a homology model
> for which i need to generate quaternary structure.
> Reply to James Strond answer
> Yes, for template structure has a quaternary structure
> and therefore are known. 
> My Query:
> How can i use these transformations for generating
> Quaternary structure? Moreover from the pdb of the
> template i also need to understand that the
> transformation are in regard to which monomer. How can
> i know that.  
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