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, 28 (1), 214-8

Kabat Database and Its Applications: 30 Years After the First Variability Plot

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Kabat Database and Its Applications: 30 Years After the First Variability Plot

G Johnson et al. Nucleic Acids Res.

Abstract

The Kabat Database was initially started in 1970 to determine the combining site of antibodies based on the available amino acid sequences at that time. Bence Jones proteins, mostly from human, were aligned, using the now-known Kabat numbering system, and a quantitative measure, variability, was calculated for every position. Three peaks, at positions 24-34, 50-56 and 89-97, were identified and proposed to form the complementarity determining regions (CDR) of light chains. Subsequently, antibody heavy chain amino acid sequences were also aligned using a different numbering system, since the locations of their CDRs (31-35B, 50-65 and 95-102) are different from those of 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 database has grown to include nucleotide sequences, sequences of T cell receptors for antigens (TCR), major histocompatibility complex (MHC) class I and II molecules and other proteins of immunological interest. It has been used extensively by immunologists to derive useful structural and functional information from the primary sequences of these proteins. An overall view of the Kabat Database and its various applications are summarized here. The Kabat Database is freely available at http://immuno.bme.nwu.edu

Figures

Figure 1
Figure 1
Variability plots for human and mouse TCR gamma and delta chain variable regions, using 377 human gamma, 1260 human delta, 297 mouse gamma and 461 mouse delta partial and complete sequences.
Figure 1
Figure 1
Variability plots for human and mouse TCR gamma and delta chain variable regions, using 377 human gamma, 1260 human delta, 297 mouse gamma and 461 mouse delta partial and complete sequences.
Figure 1
Figure 1
Variability plots for human and mouse TCR gamma and delta chain variable regions, using 377 human gamma, 1260 human delta, 297 mouse gamma and 461 mouse delta partial and complete sequences.
Figure 1
Figure 1
Variability plots for human and mouse TCR gamma and delta chain variable regions, using 377 human gamma, 1260 human delta, 297 mouse gamma and 461 mouse delta partial and complete sequences.
Figure 2
Figure 2
Length distributions of CDR3s of human and mouse TCR gamma and delta chains, based on 135 human gamma, 546 human delta, 37 mouse gamma and 66 mouse delta complete CDR3 sequences.
Figure 2
Figure 2
Length distributions of CDR3s of human and mouse TCR gamma and delta chains, based on 135 human gamma, 546 human delta, 37 mouse gamma and 66 mouse delta complete CDR3 sequences.
Figure 2
Figure 2
Length distributions of CDR3s of human and mouse TCR gamma and delta chains, based on 135 human gamma, 546 human delta, 37 mouse gamma and 66 mouse delta complete CDR3 sequences.
Figure 2
Figure 2
Length distributions of CDR3s of human and mouse TCR gamma and delta chains, based on 135 human gamma, 546 human delta, 37 mouse gamma and 66 mouse delta complete CDR3 sequences.

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