{"id":1401,"date":"2013-11-21T18:04:04","date_gmt":"2013-11-21T18:04:04","guid":{"rendered":"http:\/\/www.blopig.com\/blog\/?p=1401"},"modified":"2014-01-28T12:53:41","modified_gmt":"2014-01-28T12:53:41","slug":"annotate-antibody-cdr-and-framework-residues","status":"publish","type":"post","link":"https:\/\/www.blopig.com\/blog\/2013\/11\/annotate-antibody-cdr-and-framework-residues\/","title":{"rendered":"Annotate Antibody CDR and Framework Residues"},"content":{"rendered":"

Intro<\/strong><\/p>\n

Antibodies have very well conserved structures and their binding site is chiefly comprised of the six CDRs<\/a>. The great similarity between the 1700+ antibody structures that can be found in SAbDab\/PDB<\/a>\u00a0prompted 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<\/a>, followed by the structurally informed Chothia-scheme<\/a> which was eventually amended by Abhinandan and Martin<\/a>. Even though there are several of those schemes, the one currently endorsed by the World Health Organization (WHO<\/a>) is this of IMGT<\/a>.<\/p>\n

The Program Downolad.<\/strong><\/p>\n

It annotates the framework and CDR residues according to three definitions: Kabat, Chothia or Contact. You can download it here<\/a>.<\/p>\n

Possible issues?<\/strong><\/p>\n

You need internet connection for this program to work since it calls the Abnum<\/a> service, thus you should cite the following if you use this code:<\/p>\n

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.<\/em><\/p>\n

How to use it?<\/strong><\/p>\n

As an example test case, type the following in the Framer directory:<\/p>\n

python Framer.py --f 1A2Y.pdb --c AB --o my_first_output --d chothia<\/pre>\n
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.<\/p>\n
Options<\/strong>:<\/p>\n
–f: Antibody file
\n–c: Antibody chains (you can submit just one or several)
\n–o: Output folder name – NB this is going to be created in the directory you call Framer from!
\n–d: CDR definition to be used, possible options are: chothia, kabat and contact.<\/p>\n
Output files<\/strong>:<\/p>\n
There are four output files:<\/p>\n
red_blue.pdb: The pdb with b-factor colored CDRs. The CDRs have B-factor of 100.00 and the framework 0.00.
\nparatope.txt: The CDR residues, given in the format [id][whitespace][chain]
\nframework.txt: The Framework residues, given in the format [id][whitespace][chain]
\nfull_info.txt: Full breakdown of the annotation given in the format:<\/p>\n
Original ID Original Chain AA Chothia ID CDR(FR=frame,or CDR id)<\/pre>\n
 <\/p>\n","protected":false},"excerpt":{"rendered":"
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\u00a0prompted the introduction of numbering schemes which act as coordinates with respect to the sequence\/structural features of antibodies. The earliest such numbering scheme was […]<\/p>\n","protected":false},"author":4,"featured_media":1402,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"nf_dc_page":"","wikipediapreview_detectlinks":true,"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"ngg_post_thumbnail":0,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[29],"tags":[],"ppma_author":[482],"class_list":["post-1401","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-code"],"jetpack_featured_media_url":"https:\/\/i0.wp.com\/www.blopig.com\/blog\/wp-content\/uploads\/2013\/11\/Untitled-drawing.png?fit=950%2C378&ssl=1","jetpack_sharing_enabled":true,"authors":[{"term_id":482,"user_id":4,"is_guest":0,"slug":"konrad","display_name":"Konrad Krawczyk","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/fdb224fe7b0775e3c9a6956ae2a5ffd7c35ab8ce3ff99c5f6e0a51d45557cdd6?s=96&d=mm&r=g","0":null,"1":"","2":"","3":"","4":"","5":"","6":"","7":"","8":""}],"_links":{"self":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/1401","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/users\/4"}],"replies":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/comments?post=1401"}],"version-history":[{"count":6,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/1401\/revisions"}],"predecessor-version":[{"id":1564,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/1401\/revisions\/1564"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/media\/1402"}],"wp:attachment":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/media?parent=1401"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/categories?post=1401"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/tags?post=1401"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/ppma_author?post=1401"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}