ANARCI: antigen receptor numbering and receptor classification

By James Dunbar, Charlotte M. Deane. Bioinform., 2015

409 citations recorded by the source corpus.

Motivation: Antibody amino-acid sequences can be numbered to identify equivalent positions. Such annotations are valuable for antibody sequence comparison, protein structure modelling and engineering. Multiple different numbering schemes exist, they vary in the nomenclature they use to annotate residue positions, their definitions of position equivalence and their popularity within different scientific disciplines. However, currently no publicly available software exists that can apply all the most widely used schemes or for which an executable can be obtained under an open license. Results: ANARCI is a tool to classify and number antibody and T-cell receptor amino-acid variable domain sequences. It can annotate sequences with the five most popular numbering schemes: Kabat, Chothia, Enhanced Chothia, IMGT and AHo. Availability and implementation: ANARCI is available for download under GPLv3 license at opig.stats.ox.ac.uk/webapps/anarci. A web-interface to the program is available at the same address. Contact: deane@stats.ox.ac.uk

Subfields: Immunology, Molecular Biology, Radiology, Nuclear Medicine and Imaging

View Paper: https://www.semanticscholar.org/paper/838e4288dcef2998f78510e93f123b877ca2faa7

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Citations in the corpus

Observed Antibody Space: A diverse database of cleaned, annotated, and translated unpaired and paired antibody sequences (2021, methodology): “For each sequence, the IMGT numbering scheme was added using antibody numbering and antigen receptor classIfication (ANARCI) April 23, 2020.(33) Any sequence that ANARCI could not process was removed.”
CoV-AbDab: the Coronavirus Antibody Database (2020, methodology): “ANARCI (Dunbar and Deane (2016)) was used to number amino acid sequences in the IMGT (Lefranc et al. (2003)) numbering scheme, and to assign V and J gene origins.”
SAbPred: a structure-based antibody prediction server (2016, methodology): “Currently four applications are available: sequence numbering (18); Fv modelling including accuracy estimation and developability annotations; paratope residue prediction (14); and epitope patch prediction (15).”
TCRmodel: high resolution modeling of T cell receptors from sequence (2018, methodology): “To provide consistent residue numbering and identification of CDR loop termini, the program ANARCI (16) was used to number TCR chains.”