I didn’t find any contemporary comment on that so I’d like to ask about how to dock protein structure to dsDNA in Rosetta? Is that possible now anyhow?
I have small protein structural motif, like HTH and try to model its interaction with a sequence within dsDNA to get some hints about which residues will bind to which DNA bases so I don’t have to scan along huge DNA strands but rather have a well-defined location within the major groove to explore.
Thanks for all advice.
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