I want to do DNA protein docking. I know important residues of the protein, involved in interaction but which part of DNA is important is not clear. Also I want to provide some flexibility for docking.
Which is the best software or web server for the same? also I tried HADDOCK web server for docking, but I do not know how to select active residues as I do not know which are the important residues of DNA important for interaction? How can I perform HADDOCK docking without knowing active residues of DNA?