Abnum: Antibody numbering
08.07.08 Config files
An error in a configuration file meant that some sequences were not being numbered. This has been fixed.
This page enables you to number an antibody sequence or structure automatically using the Kabat or Chothia schemes, or our new improved Chothia scheme which includes structurally correct numbering in the framework regions.
Number your sequence
Number your structure
Apply numbering from your scripts
You may also access the numbering program directly from your scripts.
To number a sequence use a URL of the form:
http://www.bioinf.org.uk/cgi-bin/abnum/abnum.pl?plain=1&aaseq=sss&scheme=xxx
or by passing the parameters in POST format.
The fields in the URL are as follows:
| Field | Meaning |
|---|---|
| plain=1 | This causes the CGI script to generate plain parsable text rather than HTML |
| aaseq=sss | sss is the amino acid sequence |
| scheme=xxx | xxx is the numbering scheme (-k = Kabat, -c = Chothia, -a = Extended Chothia) |
To number a structure you must pass parameters in POST format and use enctype="multipart/form-data". The URL is:
http://www.bioinf.org.uk/cgi-bin/abnum/abnumpdb.pl
The fields in the URL are as follows:
| Field | Meaning |
|---|---|
| plain=1 | This causes the CGI script to generate plain parsable text rather than HTML |
| pdb=ccc | ccc is the coordinate file name |
| output=ooo | ooo is output type (-l = relabel as chains A,B,C,D, etc) |
| scheme=xxx | xxx is the numbering scheme (-k = Kabat, -c = Chothia, -a = Extended Chothia) |
The numbering program was written by Abhinandan K. Raghavan, 2006-7. For more information, or if you publish work which has used this server, please see Abhinandan, K.R. and Martin, A.C.R. (2008) Analysis and improvements to Kabat and structurally correct numbering of antibody variable domains Molecular Immunology, 45, 3832-3839. [PDF as submitted] [http://dx.doi.org/10.1016/j.molimm.2008.05.022]
