I would like to dock a ~70-residue sequence to a ~700-residue, well-ordered protein. The short sequence is likely to have a structure that ‘meanders’ over the surface of the well-ordered protein, and it’s conformation is unknown. I have ~50 chemical crosslinks (added via an unambiguous restraints file) to position the short sequence, but using a ‘standard’ HADDOCK run does not provide enough flexibility to allow this sequence to move very far away from whatever starting structure I give it. Is there a strategy to give the peptide enough flexibility to do the job here? I tried the MARTINI option, but I don’t think I really had it working well - and I wasn’t sure if I can add the unambiguous restraints when doing the docking this way.
Any advice would be appreciated.
thanks
Joel
Hi Joel
Basically you need to kind of fold your long peptide onto your protein.
You should define the peptide as fully flexible and probably increase significantly the number of steps for the it1 stages, e.g. from the default of 500/500/1000/1000 to something like 4000/4000/1000/1000.
You will have to see if this helps.
If you do it at the coarse grained level, define your unambiguous restraints to the CA / BB atoms e.g.
assign (segid A and residues XX and (name CA or name BB) (…) …