To perform DNA protein docking. we can get the active residues of the protein using HADDOCK CPORT, but I do not know how to get the active residues of DNA using Haddock server.
Please suggest some idea or any other web server to find active residues of DNA.
Hello Ambritha,
It is really difficult to perform molecular docking with an unknown binding site. I suggest you search in the literature for some information regarding your DNA motifs. Is your protein a transcription factor?
Is your DNA sequence a promoter or an enhancer? These DNA sequences, for example, contain conserved regions that are recognized by RNA polymerases.
Hello Ambritha,
Although I am a beginner myself but the HADDOCK tutorial contains pretty much all the details. You can also check the particular protein details by checking its crystal structure and analyzing the active residues. you can also check out some research papers relevant to your protein. Also if a particular protein is an antigen then you can predict its epitopes via various tools like emboss, iedb etc
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