I performed antibody-antigen docking experiments following the Rosetta antibody-antigen docking protocols. For each antibody-antigen pair, I compared the interface scores (I_sc) among the different antigens with small difference in sequence.
Here is my question: Could I compare the I_sc among antibody-antigen pairs with totally different antibodies (i.e. with different target sites on antigen)? I know it's reasonable to compare the I_sc among same antibody but different antigens with small difference in sequences, but would it still be reasonable if I compare the scores between different binding partners(i.e. different antibodies)?