Data‐driven evaluation of suitable immunogens for improved antibody selection
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Abstract
Antibodies are indispensable in laboratory and clinical applications due to their high specificity and affinity for protein antigens. However, selecting the right protein fragments as immunogens for antibody production remains challenging. Leveraging the Human Protein Atlas, this study systematically evaluates immunogen properties aiming to identify key factors that influence their suitability. Antibodies were classified as successful or unsuccessful based on standardized validation experiments, and the structural and functional properties of their immunogens were analyzed. Results indicated that longer immunogens often resulted in more successful but less specific antibodies. Shorter immunogens (50 residues or fewer) with disordered or unfolded regions at the N‐ or C‐terminus and long coil stretches were more likely to generate successful antibodies. Conversely, immunogens with high beta sheet content, transmembrane regions, or disulfide bridges were associated with poorer antibody performance. Post‐translational modification sites within immunogens appeared to mark beneficial regions for antibody generation. To support antibody selection, a novel R package, immunogenViewer, was developed, enabling researchers to easily apply these insights when immunogen sequences are disclosed. By providing a deeper understanding of immunogen suitability, this study promotes the development of more effective antibodies, ultimately addressing issues of reproducibility and reliability in antibody‐based research. The findings are highly relevant to the research community, as end users often lack control over the immunogen selection process in antibody production. The R package is freely available as part of Bioconductor: https://bioconductor.org/packages/release/bioc/html/immunogenViewer.html .
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Zhou, M., Ji, S.-W., Zhang, L., Chen, C.-C., Wu, Z., Cao, S.-N., & Zhu, S.-Y. (2026) · Pathogens · doi:10.3390/pathogens15090983
“These candidates were selected based on high genotypic conservation, strong predicted antigenicity, and favorable expression characteristics [25–28], and can be efficiently produced in E. coli at reduced cost.”
- Authors
- Waury, K., Kvartsberg, H., Zetterberg, H., Blennow, K., Teunissen, C. E., & Abeln, S.
- Affiliations
- Utrecht University (NL)
- Sahlgrenska University Hospital (SE)
- University of Wisconsin System (US)
- University of Science and Technology of China (CN)
- Amsterdam Neuroscience (NL)
- Corresponding author
- Abeln, Sanne
- ORCID
- Venue
- Protein Science
- Publisher
- Wiley
- Published
- 2025-03-21
- Volume
- 34
- Issue
- 4
- Pages
- e70100-e70100
- ISSN
- 0961-8368 (ISSN-L)
- 1469-896X
- PMC
- PMC11926642
- OpenAlex
- W4408745641
- Cited by
- 1
- References
- 41
- Citations by year
- 2026: 1
- FWCI
- 0.57
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Protein Science (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Pure Amsterdam UMC (publishedVersion, other-oa)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- Funders
- Netherlands eScience Center
- Alzheimer Nederland
- Horizon 2020 Framework Programme (860197, 101053962, 22HLT07, 831434)
- Vetenskapsrådet (2017‐00915, 2022‐00732, 2023‐00356, 2022‐01018, 2019‐02397)
- Alzheimerfonden (AF‐930351, AF‐939721, AF‐968270, AF‐994551)
- Hjärnfonden (FO2017‐0243, ALZ2022‐0006, FO2022‐0270)
- EU Joint Programme – Neurodegenerative Disease Research (JPND2019‐466‐236, JPND2021‐00694)
- Alzheimer's Association (ZEN‐21‐848495, SG‐23‐1038904 QC, ADSF‐21‐831376‐C, ADSF‐21‐831381‐C, ADSF‐21‐831377‐C, ADSF‐24‐1284328‐C)
- Fondation pour la Recherche sur Alzheimer
- Kirsten og Freddy Johansens Fond
- Alzheimer's Drug Discovery Foundation (201809‐2016862)
- European Partnership on Metrology
- UK Dementia Research Institute (UKDRI‐1003)
- ZonMw (73305095007, 10510032120003)
- 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 Structure and Dynamics
- Keywords
- antibody production, antibody specificity, protein disorder, coil regions, β-sheet content, transmembrane domain, disulfide bonds, post-translational modification sites, Human Protein Atlas, R package, Bioconductor
- MeSH terms
- Antibodies, Antigens, Humans, Databases, Protein
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