AgAbDb, a derived knowledge base, archives molecular interactions of protein and peptide antigens characterized by co-crystal structures. The interactions are compiled at two levels, viz. residue level and atomic level. The interactions are characterized using AAIF (Antigen-Antibody Interaction Finder) developed in-house. AAIF enlists various non-covalent interactions such as van der Waals, salt bridges, hydrogen bonds and short contacts using distance and geometry-based criteria. Apart from molecular interactions, AgAbDb also archives information pertaining to Ag and Ab description, definition of Complementarity Determining Regions on light chain (LDR) and Complementarity Determining Regions on heavy chain (CDR) residues of the antibody with both, the PDB as well as Wu and Kabat numbering.
The database contains 551* antigen-antibody complexes.
• 389 Protein-Ab complexes
• 162 Peptide-Ab complexes
*as on Mon Nov 30 15:45:00 IST 2020