hello, I am trying dock a protein onto a nucleosome. I tidied up all the format and everything goes well in the “input data” part. But in the “input parameters”, it requires me to have the active residues stated for both the protein and nucleosome. I know which part of the protein is involved in but I do not know the active residues of the nucleosome as that is part of what I want to find out through this docking. Is it possible to do this docking only knowing the active residues of the protein?
Or is it because I choose wrong in the type in “input data”
I choose “protein/protein ligand” for my protein
and I choose “ligand” for my nucleosome
Thank you.
Hi Kevin
For the nucleosome choose protein-nucleic acid. But make sure there is no overlap in numbering between the various components of the nucleosome (this might require some renumbering of residues).
As for the active residues, if you don’t know anything on the nucleosome side (do you know if the protein bind to the protein or the DNA), use the option to define the entire surface as passive. This will however be quite expensive in terms of computing time.
Thank you!