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

Please enter the Light Chain or Heavy Chain amino acid sequence of your antibody (single letter code)

Select the numbering scheme you wish to apply:

Kabat
Chothia
Chothia with structurally corrected framework indels


Number your structure

Upload the PDB file:
Select the numbering scheme:
Kabat
Chothia
Chothia with structurally corrected framework indels
Output: Label as LH   Label as AB
  To screen   To a PDB file


Apply numbering from your scripts

You may also access the numbering program directly from your scripts using our simple REST-style web-services interface.

Numbering sequences

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:

FieldMeaning
plain=1This causes the CGI script to generate plain parsable text rather than HTML
aaseq=ssssss is the amino acid sequence
scheme=xxxxxx is the numbering scheme (-k = Kabat, -c = Chothia, -a = Extended Chothia)

You can download a sample Perl script that uses the web services-interface to Abnum.

Numbering structures

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:

FieldMeaning
plain=1This causes the CGI script to generate plain parsable text rather than HTML
pdb=cccccc is the coordinate file name
output=oooooo is output type (-l = relabel as chains A,B,C,D, etc)
scheme=xxxxxx 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]

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.