Kabat Database and its applications: 30 years after the first variability plot

The Kabat Database was initially started in 1970 to determine the combining site of antibodies based on the available amino acid sequences at that tim e. Bence Jones proteins, mostly from human, were aligned, using the now-kno wn Kabat numbering system, and a quantitative measure, variability, was cal culated for every position. Three peaks, at positions 24-34, 50-56 and 89-9 7, were identified and proposed to form the complementarity determining reg ions (CDR) of light chains. Subsequently, antibody heavy chain amino acid s equences were also aligned using a different numbering system, since the lo cations of their CDRs (31-35B, 50-65 and 95-102) are different from those o f the light chains. CDRL1 starts right after the first invariant Cys 23 of light chains, while CDRH1 is eight amino acid residues away from the first invariant Cys 22 of heavy chains. During the past 30 years, the Kabat datab ase has grown to include nucleotide sequences, sequences of T cell receptor s for antigens (TCR), major histocompatibility complex (MHC) class I and II molecules and other proteins of immunological interest, It has been used e xtensively by immunologists to derive useful structural and functional info rmation from the primary sequences of these proteins, An overall view of th e Kabat Database and its various applications are summarized here, The Kaba t Database is freely available at http://immuno. bme.nwu.edu.