I am using HADDOCK’s easy interface to dock a modelled antibody structure to its antigen structure. I am planning keep the CDR3 loop of the antibody heavy chain fully flexible in the docking procedure to obtain better results. Can you please kindly guide me how can I do it ? I read it on the run.cns but I am not clear about it.
On the expert interface, under semi-flexible segments section, I should choose the ‘full’ option, and then, I should put the number of the initial and the last residue of the loops. Is this correct ?