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
>
> --
>
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> Michael Sierk email:
> Pharmacology Dept./Biophysics Program Phone(W): (804) 243-6725/924-1953
> Box 800735, Health Sciences Center (H): (804) 970-2268
> University of Virginia Fax: (804) 924-9057
> http://www.people.virginia.edu/~mls5w
> GBS Homepage: http://www.med.virginia.edu/ed-programs/gpo/gbs/
> Grad Council Homepage: http://www.student.virginia.edu/~gsasc/
> ------------------------------------------------------------------------
> "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