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: mls5w@virginia.edu > 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 sali@rockefeller.edu; http://salilab.org