[modeller_usage] modeling protein-DNA complex

[Betty Shen <bshen AT fhcrc.org>]

Hi modellers,

I would like to build a model of a protein-dna complex based on the 
x-ray structure of a homologous protein in a
protein-dna complex  I would use the exact DNA sequence in the model 
just to provide some constrain on the protein.
I noticed that there are nucleotides in the restyp.lib.  But I cannot 
find examples on how to enter DNA sequence in the align.ali file.  Has 
anybody tried modelling with DNA in MODELLER?

I would appreciate it very much if someone can give me some or point me 
to where I can find some examples.

Thanks a bunch in advance.

Betty

Betty Shen
Fred Hutchinson Cancer Research Center