The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to http://www.bonvinlab.org/software/haddock2.2
Dear Alexandre and HADDOCK users,
I want to do protein -dna docking by haddock2.2. The situation in my case is :
1) The interaction between my protein A and DNA is weak. The DNA binding sites on protein A can be mapped through NMR titration and the structure of protein A has been solved. But the protein A binding sites on DNA can not be verified.
2) To solve the problem of 1), we found that peptide B can tightly bind with DNA in the minor groove. The structure of peptide B with DNA is known. Then we linked protein A with peptide B and got the protein A- peptide B by expression.
But we failed to detect inter-NOES between protein and DNA.
My question is how I can do the docking between protein A and the complex of peptide B-DNA by HADDOCK2.2.
I know that there is a multi-body docking mode in HADDOCK2.2. But as described above, the protein A and peptide B has been integrated into a whole protein and the peptide B is flexible in solution and no interaction with protein A. The orientation of the protein A should be limited by the existence of peptide B, not like separately docking.
In that case, how can I do the docking with the peptide B-DNA complex using protein A?
Thanks in advance.