Canonicals - Chothia Canonical Assignment

This page allows you to identify the Chothia canonical classes of CDRs L1, L2, L3, H1 and H2 from an antibody sequence. When a CDR does not match a canonical class, the most similar class will be displayed and mismatching residues which caused the assignment to fail will be displayed.

Three sets of results will be given. The key residue requirements for each set are defined in a datafile. In these datafiles, the key residue positions are shown with the allowed amino acids at each position. The sequence which you supply is first aligned with a consensus antibody sequence to assign the Kabat numbering scheme. (Some of the datafiles use the Chothia numbering scheme; in these cases conversion between the numbering schemes is handled automatically.) The method used to do this is the same as that used by the sequence testing facility.

The first set of results uses a set of key residue templates derived by a new automated method (Martin and Thornton, (1996) Structural families of loops in homologous proteins: Automatic classification, modelling and application to antibodies. J. Mol. Biol., 263, 800-815). These results are likely to be the most accurate, but since the templates are more restrictive, there are likely to be more sequences which cannot be predicted. Datafile.

The second set of results come from a set of key residues used by Oxford Molecular's AbM software. These are based on the key residues presented by Chothia et al., but have a few additional required and allowed residues. A few additional classes have also been defined. Datafile.

The final set of results comes from strict application of the templates which appear in a number of papers by Chothia et al. Definitions from various papers have been merged to create this template set. There is some slight confusion over the numbering of classes as Chothia has described classes without giving them "official" numbers. Currently, classes are numbered in the order in which they are described with a note where appropriate if a later paper uses a different number. This may change soon. Datafile.

If you get any error or warning messages, please check you have entered your sequence correctly. Strange sequence features may cause the alignment stage to fail. Loops longer than anything observed in the current Kabat database will also cause the alignment to fail. If, after checking your sequence, you still get errors or warnings, please send me EMail: and I'll see if the programs can be modified to accomodate your sequence. Alternatively, your antibody may just be very strange!

Test your sequence against the Kabat sequence database.

Enter the amino acid sequence (1-letter code) of your Fv (optionally you may include the whole Fab fragment, but only the Fv portion will be tested).

Enter the light chain amino acid sequence here:

Enter the heavy chain amino acid sequence here:

Please enter your EMail address here:

Return the Kabat numbered sequence as well as the canonical definitions?


Commercial Use

Companies may use this public server, but need to be aware that data are not encrypted and it is not secure.

After trialing the system, companies should consider abYsis. A commercial licence will enable you to install a local version of this code together with an integrated database which can also store and analyse proprietary sequence and structure data.

For information on commercial licences, please contact the distributor Ebisu.