Citing¶
If you use antibody-utils in published work, please cite it, and the methods and data it implements that your work relies on.
antibody-utils¶
antibody-utils is developed by the
Oxford Protein Informatics Group. Each
release is archived on Zenodo. Cite antibody-utils
with its DOI,
10.5281/zenodo.23242278,
which always resolves to the latest release. Zenodo’s page for it also lists
a DOI for each version, if you need to cite the one you used. The repository’s
CITATION.cff gives the same citation, and GitHub’s Cite this repository
button formats it in APA or BibTeX.
Methods and data¶
If you use |
Please cite |
|---|---|
Numbering with ANARCII ( |
Greenshields-Watson A, Agarwal P, Robinson SA, Williams BH, Gordon GL, Capel HL, Li Y, Spoendlin FC, Boyles F and Deane CM, ANARCII: a generalised language model for antigen receptor numbering, bioRxiv (2025) |
The IMGT scheme or definition |
Lefranc M-P et al., IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains, Dev Comp Immunol 27:55–77 (2003) |
Other schemes and definitions |
The references in Numbering schemes and region definitions |
|
Henikoff S and Henikoff JG, Amino acid substitution matrices from protein blocks, Proc Natl Acad Sci USA 89:10915–10919 (1992) |
|
Dunbar J, Fuchs A, Shi J and Deane CM, ABangle: characterising the VH–VL orientation in antibodies, Protein Eng Des Sel 26:611–620 (2013) |
Structures (read with GEMMI) |
Wojdyr M, GEMMI: a library for structural biology, J Open Source Softw 7:4200 (2022) |
Structure files from SAbDab |
Dunbar J, Krawczyk K, Leem J, Baker T, Fuchs A, Georges G, Shi J and Deane CM, SAbDab: the structural antibody database, Nucleic Acids Res 42:D1140–D1146 (2014); and Capel HL, Vavourakis O, Williams BH, Taylor CR and Deane CM, SAbDab2: the structural antibody database in the age of machine learning, bioRxiv (2026) |