Annotate Antibody CDR and Framework Residues

Intro

Antibodies have very well conserved structures and their binding site is chiefly comprised of the six CDRs. The great similarity between the 1700+ antibody structures that can be found in SAbDab/PDB prompted the introduction of numbering schemes which act as coordinates with respect to the sequence/structural features of antibodies. The earliest such numbering scheme was introduced by Wu and Kabat, followed by the structurally informed Chothia-scheme which was eventually amended by Abhinandan and Martin. Even though there are several of those schemes, the one currently endorsed by the World Health Organization (WHO) is this of IMGT.

The Program Downolad.

It annotates the framework and CDR residues according to three definitions: Kabat, Chothia or Contact. You can download it here.

Possible issues?

You need internet connection for this program to work since it calls the Abnum service, thus you should cite the following if you use this code:

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.

How to use it?

As an example test case, type the following in the Framer directory:

python Framer.py --f 1A2Y.pdb --c AB --o my_first_output --d chothia

This should get the the heavy and light chains of 1A2Y (A and B) and leave the output in a folder called my_first_outupt.

Options:

–f: Antibody file
–c: Antibody chains (you can submit just one or several)
–o: Output folder name – NB this is going to be created in the directory you call Framer from!
–d: CDR definition to be used, possible options are: chothia, kabat and contact.

Output files:

There are four output files:

red_blue.pdb: The pdb with b-factor colored CDRs. The CDRs have B-factor of 100.00 and the framework 0.00.
paratope.txt: The CDR residues, given in the format [id][whitespace][chain]
framework.txt: The Framework residues, given in the format [id][whitespace][chain]
full_info.txt: Full breakdown of the annotation given in the format:

Original ID Original Chain AA Chothia ID CDR(FR=frame,or CDR id)

 

Leave a Reply