Antibody Annotation - A simple to use Python script annotating VH or VL sequences of an antibody using Kabat, Chothia, Contact, or IMGT schemes. It utilizes the REST API interface of Abnum from Dr Andrew Martin's group at UCL
User provides a single-letter amino acid sequence of the VH or VL chain of an antibody, and specifies an annotation scheme (Kabat, Chothia, or Contact, or IMGT). The script sends a request to Abnum, which returns a string with each residue matched to its number. The script then identifies FR and CDR regions using definitions outlined here1. It prints out the amino acid sequence of the FRs and CDRs, and returns a list of 2 dict. The first dict consists of region: seq pairs. The second dict consists of number:residue pairs.
1Definitions for Kabat, Chothia, Contact, and IIMGT are same as listed in the table, except that for IMGT, H-CDR2 is defined as H51-H57 in this script, as opposed to of H51-H56 in the table. This slight revision generates result that matches that from IMGT website
- Imports
requestsmodule
aaseq: STRING amino acid sequence, single-letter coded, needs to be complete VH OR VL sequence. Upper/lower case.
scheme:STRING annotation scheme, can be one of the following: "kabat", "chothia", "contact", "imgt". Must be lowercase
aaseq="EIVLTQSPAIMSASPGERVTMTCSASSGVNYMHWYQQKPGTSPRRWIYDTSKLASGVPARFSGSGSGTDYSLTISSMEPEDAATYYCHQRGSYTFGGGTKLEIK"
scheme="chothia"
seq=annotate(aaseq,scheme)result=seq.retrieve()
print(result[0]) #prints the first dict (region vs seq)
print(result[1]) #prints the second dict (number vs residue)Annotation in Chothia scheme:
L-FR1: EIVLTQSPAIMSASPGERVTMTC
L-CDR1: SASSGVNYMH
L-FR2: WYQQKPGTSPRRWIY
L-CDR2: DTSKLAS
L-FR3: GVPARFSGSGSGTDYSLTISSMEPEDAATYYC
L-CDR3: HQRGSYT
L-FR4: FGGGTKLEIK
{'L-FR1': 'EIVLTQSPAIMSASPGERVTMTC', 'L-CDR1': 'SASSGVNYMH', 'L-FR2': 'WYQQKPGTSPRRWIY', 'L-CDR2': 'DTSKLAS', 'L-FR3': 'GVPARFSGSGSGTDYSLTISSMEPEDAATYYC', 'L-CDR3': 'HQRGSYT', 'L-FR4': 'FGGGTKLEIK'}
{'L1': 'E', 'L2': 'I', 'L3': 'V', 'L4': 'L', 'L5': 'T', 'L6': 'Q', 'L7': 'S', 'L8': 'P', 'L9': 'A', 'L10': 'I', 'L11': 'M', 'L12': 'S', 'L13': 'A', 'L14': 'S', 'L15': 'P', 'L16': 'G', 'L17': 'E', 'L18': 'R', 'L19': 'V', 'L20': 'T', 'L21': 'M', 'L22': 'T', 'L23': 'C', 'L24': 'S', 'L25': 'A', 'L26': 'S', 'L27': 'S', 'L28': 'G', 'L29': 'V', 'L30': 'N', 'L32': 'Y', 'L33': 'M', 'L34': 'H', 'L35': 'W', 'L36': 'Y', 'L37': 'Q', 'L38': 'Q', 'L39': 'K', 'L40': 'P', 'L41': 'G', 'L42': 'T', 'L43': 'S', 'L44': 'P', 'L45': 'R', 'L46': 'R', 'L47': 'W', 'L48': 'I', 'L49': 'Y', 'L50': 'D', 'L51': 'T', 'L52': 'S', 'L53': 'K', 'L54': 'L', 'L55': 'A', 'L56': 'S', 'L57': 'G', 'L58': 'V', 'L59': 'P', 'L60': 'A', 'L61': 'R', 'L62': 'F', 'L63': 'S', 'L64': 'G', 'L65': 'S', 'L66': 'G', 'L67': 'S', 'L68': 'G', 'L69': 'T', 'L70': 'D', 'L71': 'Y', 'L72': 'S', 'L73': 'L', 'L74': 'T', 'L75': 'I', 'L76': 'S', 'L77': 'S', 'L78': 'M', 'L79': 'E', 'L80': 'P', 'L81': 'E', 'L82': 'D', 'L83': 'A', 'L84': 'A', 'L85': 'T', 'L86': 'Y', 'L87': 'Y', 'L88': 'C', 'L89': 'H', 'L90': 'Q', 'L91': 'R', 'L92': 'G', 'L93': 'S', 'L96': 'Y', 'L97': 'T', 'L98': 'F', 'L99': 'G', 'L100': 'G', 'L101': 'G', 'L102': 'T', 'L103': 'K', 'L104': 'L', 'L105': 'E', 'L106': 'I', 'L107': 'K'}
- Relies on internet connection to Abnum website
- Currently it can only annotate using Kabat, Chothia, or Contact, or IMGT scheme. One scheme each time.
- Incomplete VH or VL sequence might not be annotated