We want to find all possible epitopes (against human IgA, IgG, IgM, IgE
in the PDB structure 2AIZ, whose sequence is:
This requires a multi-step process (we are still working on a more direct way of doing this).
First, perform a "B cell search" (under the search menu), and pull out all epitopes that match your criteria except for the sequence bit. That means host organism = 'homo sapiens', under assayed antibody, click on all isotypes you want (IgA, IgG, IgM, IgE and IgD). From the query results, choose the positive peptides (I got 6,909). Export the results into an Excel sheet using the button over the results table.
Second, use Excel (or the script language of your choice), to check for each peptide sequence if it is found in the protein sequence you are interested in.