Epitome - Database of Structurally inferred Antigenic Epitopes in Proteins

To compile this database, we aligned all available structures of antibodies and analyzed them to identify CDRs. Based on this analysis we found all the proteins in PDB that are bound to an antibody, and identified within them the residues that bind to CDRs.

Each entry in the database describes one interaction between a residues on an antigenic protein and a residues on an antibody chain. Every interaction is described using the following parameters: (1) PDB ID (2) PDB chain ID of the antigenic protein (3) PDB position of the antigenic residue (4) type of antigenic residue and its sequence environment (5) PDB chain ID of the antibody chain (6) type of antibody chain (heavy or light) (7) CDR number (8) PDB position of the antibody residue (9) type of antibody residue and its sequence environment.

You can search the database using any of those parameters.
For example: you can look for all the antigenic residues in the hen lysozyme 1a2y_C.
The query would be: pdb_id=1a2y, antigen chain=C. all the other fields left blank.
Results: A list of all the residues in 1a2y_C that are in an *antigenic* contact with the antibody (note: in each antibody-protein interaction we distinguish between antigenic interactions and non-antgenic ones).
In the results pages you can click on the PDB ID and open a java application that will show the 3D structure of the complex with coloring of the interacting residues.

Another example:
Find all the antigenic interaction where there is an Arginine is CDR1 on the light chain. The query would be: pdb_id=all, Chain Type= light, antibody residue=R, CDR=1.

You can also search on any other combination of parameters (e.g. find all the known antigenic interactions between a particular pair of residues) etc.

If your protein of interest does not have a know complex with an antibody, you can enter its sequence and BLAST it against all the sequences in the database. The results would be all the known 3-D complexes between antibodies and proteins that are similar to the query sequence.

Avner Schlessinger