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Re: Protein:DNA complexes in Modeller



Mike Sierk wrote:
> 
> Dr. Sali,
> 
> We do not have Modeller installed here, and I was wondering how it does
> modelling DNA-binding proteins.  I have a structure of a protein:DNA
> complex and would like to make a model of a related protein.  Would it
> work to just use the protein structure as a template, ignoring the DNA?

Yes.

> Could it model the unknown protein on the known DNA structure? 

Yes, but not with the default protocol.

> Would it
> model the unknown protein:DNA complex(with a different DNA sequence)
> using the known complex?

Yes, but not with the default protocol. The results are not likely to be
overwhelming.

Best, Andrej

> 
> I found only two questions about DNA in the archive, with no answers to
> either.
> 
> Thank you,
> Michael Sierk
> 
> --
> 
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> Michael Sierk                               email: 
> Pharmacology Dept./Biophysics Program    Phone(W): (804) 243-6725/924-1953
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> University of Virginia                        Fax: (804) 924-9057
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> ------------------------------------------------------------------------
> "If at first you do succeed, try not to act surprised."
>     - Anonymous.
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

--
Andrej Sali, Associate Professor
The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399
tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540
e-mail ; http://salilab.org