Structurally mapping antibody repertoires
Open accessAbstract
next-generation sequencing of immunoglobulin genes (Ig-seq). This technique produces large volume sequence snapshots of B-cell receptors that are indicative of the antibody repertoire. In this paper, we enrich these large-scale sequence datasets with structural information. Enriching a sequence with its structural data allows better approximation of many vital features, such as its binding site and specificity. Here, we describe the structural annotation of antibodies pipeline that maps the outputs of large Ig-seq experiments to known antibody structures. We demonstrate the viability of our protocol on five separate Ig-seq datasets covering ca. 35 m unique amino acid sequences from ca. 600 individuals. Despite the great theoretical diversity of antibodies, we find that the majority of sequences coming from such studies can be reliably mapped to an existing structure.
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Human antibody repertoires appear to be constrained structurally, including regions of the antibody that display great variability such as the CDRH3 loop.
“Human antibody repertoires also appear to be constrained structurally, and this includes regions of the antibody that display great variability such as the CDRH3 loop [224].”
From Computational approaches to therapeutic antibody design: established methods and emerging trends (2020) · cites this paper as [224]
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- Authors
- Krawczyk, K., Kelm, S., Kovaltsuk, A., Galson, J. D., Kelly, D., Trück, J., Regep, C., Leem, J., Wong, W. K., Nowak, J., Snowden, J., Wright, M., Starkie, L., Scott-Tucker, A., Shi, J., & Deane, C. M.
- Affiliations
- University of Oxford (GB)
- UCB Pharma (United Kingdom) (GB)
- University Children's Hospital Zurich (CH)
- Corresponding author
- Deane, Charlotte M.
- ORCID
- Venue
- Frontiers in Immunology
- Publisher
- Frontiers Media SA
- Published
- 2018-07-23
- Volume
- 9
- Pages
- 1698-1698
- ISSN
- 1664-3224 (ISSN-L)
- PMC
- PMC6064724
- OpenAlex
- W2884483443
- Cited by
- 42
- References
- 47
- Citations by year
- 2026: 3 · 2025: 4 · 2024: 5 · 2023: 3 · 2022: 3 · 2021: 4 · 2020: 7 · 2019: 10 · 2018: 3
- FWCI
- 4.11
- 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)
- Zurich Open Repository and Archive (University of Zurich) (acceptedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Zurich Open Repository and Archive (University of Zurich) (submittedVersion, cc-by)
- Zurich Open Repository and Archive (University of Zurich)
- Funders
- Directorate for Biological Sciences
- Engineering and Physical Sciences Research Council (1762010, EP/G037280/1)
- Biotechnology and Biological Sciences Research Council (1801486, BB/M011224/1, M011224)
- 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 › Immunology and Microbiology › Immunology › T-cell and B-cell Immunology
- Keywords
- antibody repertoire, B cell receptor, binding site prediction, antibody specificity, antibody diversity
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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