[modeller_usage] modeling protein-DNA complex

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