I am studying antigen-antibody interaction at protein level. I have a protein sequence (no crystal structure) of the antigen, and have predicted the secondary structure of it. By performing conserved domain search using inferno and NCBI I found out a domain in the antigen - PCC1. I am interested to know how the antigen interacts with the antibody (2000 residues) in silico. The ultimate aim is to find out "how the antigen interacts with the antibody, and predict the possible domains used by the antigen to interact with the antibody". I would really appreciate your valuable suggestions.
Thanks much, DK