Numbering Schemes

Five numbering schemes are now implemented within abYsis:

• Kabat: Most widely adopted standard but positions at which insertions occur in CDR-L1 and CDR-H1 do not match the structural insertion positions.
• Chothia: similar to the Kabat but places CDR-L1 and CDR-H1 insertions at the structurally correct positions.
• Martin: enhanced version of the Chothia scheme that place Framework insertions and deletions at structurally correct positions.
• IMGT: Implementation of an IMGT numbering scheme. Pre-defines theoretically longest possible loops
• Aho: Structurally defined numbering. Similar to IMGT but ensures structurally accurate insertion and deletion positions.

CDR/Framework Scheme

Five CDR definitions are now supported:

• Kabat, based on sequence variability.
• Chothia, based on the location of the structural loop regions. (Note that Chothia definition has varied between different papers – this is the one judged to be most relevant.
• AbM Compromise between the Kabat and Chothia. Whitelegg N & Rees AR, Protein Eng. 13(2000):819-824 Methods Mol Biol. 248(2004)51-91).
• Contact: Based on an analysis of which residues contact antigen in crystal structures. (MacCallum RM, Martin ACR & Thornton JM, J. Mol. Biol. 262(1996)732-745).
• IMGT: CDR and Framework definitions as defined by IMGT

Note
Chothia region definition for CDR-H1 loop, and Contact definition for CDR-L1 loop, have a complex specification when using the Kabat numbering scheme. However, for a given sequence, the CDR regions are ultimately independent of the numbering scheme. Internally, abYsis prioritises the Chothia numbering scheme to delineate regions.