Antibody Mode Tutorial

Our lab has developed a special mode for use with antibody docking that has been optimized on version 1 of the Protein-Protein Docking Benchmark. The results and methods of this mode have been described in this paper by Brenke et al. If you know your complex is composed of an antibody and antigen, this mode will produce much better results.

  1. In antibody mode, you will need to specify the identity of the antibody and antigen by placing the antibody as the receptor and the antigen as the ligand. You can see below, we have used the first antibody-antigen case in Version 3 of the Protein-Protein Docking Benchmark, where 1fgn is the antibody and 1tfh is the antigen.
  2. For the server to treat this an antibody case, you will need to click on "Advanced Options" and then "Antibody Mode". You can then check the body to indicate using antibody mode.
  3. In antibodies, binding usually occurs to the complementarity-determining regions (CDRs). Thus, your docking results can be improved if you mask those residues that do not fall in the CDR. You can find details on how to make a masking file in our Attraction and Repulsion Tutorial. You can find how to determine the CDRs using this tutorial or the Abysis server.

If you have any questions, please look to see if it is addressed on the help page. If you have any suggestions, please contact us.

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Vajda Lab and ABC Group
Boston University and Stony Brook University