Understanding the significance and implications of antibody numbering and antigen-binding surface/residue definition
Open accessAbstract
Monoclonal antibodies are playing an increasing role in both human and animal health. Different strategies of protein and chemical engineering, including humanization techniques of non-human antibodies were applied successfully to optimize clinical performances of antibodies. Despite the emergence of techniques allowing the development of fully human antibodies such as transgenic Xeno-mice, antibody humanization remains a standard procedure for therapeutic antibodies. An important prerequisite for antibody humanization requires standardized numbering methods to define precisely complementary determining regions (CDR), frameworks and residues from the light and heavy chains that affect the binding affinity and/or specificity of the antibody-antigen interaction. The recently generated deep-sequencing data and the increasing number of solved three-dimensional structures of antibodies from human and non-human origins have led to the emergence of numerous databases. However, these different databases use different numbering conventions and CDR definitions. In addition, the large fluctuation of the variable chain lengths, especially in CDR3 of heavy chains (CDRH3), hardly complicates the comparison and analysis of antibody sequences and the identification of the antigen binding residues. This review compares and discusses the different numbering schemes and "CDR" definition that were established up to date. Furthermore, it summarizes concepts and strategies used for numbering residues of antibodies and CDR residues identification. Finally, it discusses the importance of specific sets of residues in the binding affinity and/or specificity of immunoglobulins.
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Similarities between antibody amino acid sequences further allow for the creation of a standardized reference framework, or numbering scheme, giving each variable region amino acid an identifier.
“Similarities between antibody amino acid sequences further allow for the creation of a standardized reference framework, or numbering scheme, giving each variable region amino acid an identifier [151].”
From Computational approaches to therapeutic antibody design: established methods and emerging trends (2020) · cites this paper as [151]
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Computational approaches to therapeutic antibody design: established methods and emerging trends
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“Similarities between antibody amino acid sequences further allow for the creation of a standardized reference framework, or numbering scheme, giving each variable region amino acid an identifier [151].”
BackgroundSaka, K., Kakuzaki, T., Metsugi, S., Kashiwagi, D., Yoshida, K., Wada, M., Tsunoda, H., & Teramoto, R. (2021) · Scientific Reports · doi:10.1038/s41598-021-85274-7 · Cited by 144 · see citing works
- Authors
- Dondelinger, M., Filée, P., Sauvage, E., Quinting, B., Muyldermans, S., Galleni, M., & Vandevenne, M. S.
- Affiliations
- University of Liège (BE)
- European Remanufacturing Council (BE)
- Haute École Libre Mosane (BE)
- Vrije Universiteit Brussel (BE)
- Corresponding author
- Dondelinger, Mathieu
- Vandevenne, Marylène S.
- Venue
- Frontiers in Immunology
- Publisher
- Frontiers Media SA
- Published
- 2018-10-16
- Volume
- 9
- Pages
- 2278-2278
- ISSN
- 1664-3224 (ISSN-L)
- PMC
- PMC6198058
- OpenAlex
- W2890382137
- Cited by
- 107
- References
- 96
- Citations by year
- 2026: 6 · 2025: 16 · 2024: 25 · 2023: 11 · 2022: 11 · 2021: 19 · 2020: 12 · 2019: 7
- FWCI
- 1.48
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Frontiers in Immunology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Open Repository and Bibliography (University of Liège) (submittedVersion, other-oa)
- VUBIR (Vrije Universiteit Brussel) (submittedVersion)
- Funders
- Waalse Gewest
- Topics
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Monoclonal and Polyclonal Antibodies Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein purification and stability
- Keywords
- hypervariable region, CDR3, antibody humanization, antigen-antibody reaction, antibody database, binding affinity, binding specificity, therapeutic antibodies
- MeSH terms
- Protein Domains, Amino Acid Sequence, Amino Acids, Animals, Antibodies, Monoclonal, Humans, Immunoglobulin Heavy Chains, Immunoglobulin Light Chains, Complementarity Determining Regions, Mice
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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