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[modeller_usage] modeling protein-DNA complex

To: "'Modeller Care'" <modeller-care@salilab.org>, <modeller_usage@salilab.org>
Subject: [modeller_usage] modeling protein-DNA complex
From: Betty Shen <bshen@fhcrc.org>
Date: Tue, 2 Mar 2004 19:11:05 -0800

Hi modellers,

I would like to build a model of a protein-dna complex based on thex-ray structure of a homologous protein in aprotein-dna complex I would use the exact DNA sequence in the modeljust to provide some constrain on the protein.I noticed that there are nucleotides in the restyp.lib. But I cannotfind examples on how to enter DNA sequence in the align.ali file. Hasanybody tried modelling with DNA in MODELLER?

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

Thanks a bunch in advance.

Betty

Betty Shen
Fred Hutchinson Cancer Research Center

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