ArticleFrontiers in immunology2023
A comparison of the binding sites of antibodies and single-domain antibodies.
Article in Frontiers in immunology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 37 citations in OpenAlex.
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- Characterising nanobody developability to improve therapeutic design using the Therapeutic Nanobody Profiler.Communications biology · 2026Article
- uPAR-directed immunotherapies in solid tumors: current advances and future perspectives.Frontiers in pharmacology · 2026Review
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- Nanodesigner: resolving the complex-CDR interdependency with iterative refinement.Journal of cheminformatics · 2025Article
- Nanobodies: From Discovery to AI-Driven Design.Biology · 2025Review
- Single-Domain Antibodies That Specifically Recognize Intact Capsids of Multiple Foot-and-Mouth Disease Serotype O Strains.Vaccines · 2025Article
- Article
- Improved prediction of antibody and their complexes with clustered generative modelling ensembles.Bioinformatics advances · 2025Article
- Comparative analysis of CDR3 length-dependent patterns in VHHs.Frontiers in immunology · 2025Article
- Structural trends in antibody-antigen binding interfaces: a computational analysis of 1833 experimentally determined 3D structures.Computational and structural biotechnology journal · 2024Article
- On the humanization of VHHs: Prospective case studies, experimental and computational characterization of structural determinants for functionality.Protein science : a publication of the Protein Society · 2024Article
- The Patent and Literature Antibody Database (PLAbDab): an evolving reference set of functionally diverse, literature-annotated antibody sequences and structures.Nucleic acids research · 2024Article
- Distinct types of VHHs in Alpaca.Frontiers in immunology · 2024Article
- nanoBERT: a deep learning model for gene agnostic navigation of the nanobody mutational space.Bioinformatics advances · 2024Article
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
Antibodies are the largest class of biotherapeutics. However, in recent years, single-domain antibodies have gained traction due to their smaller size and comparable binding affinity. Antibodies (Abs) and single-domain antibodies (sdAbs) differ in the structures of their binding sites: most significantly, single-domain antibodies lack a light chain and so have just three CDR loops. Given this inherent structural difference, it is important to understand whether Abs and sdAbs are distinguishable in how they engage a binding partner and thus, whether they are suited to different types of epitopes. In this study, we use non-redundant sequence and structural datasets to compare the paratopes, epitopes and antigen interactions of Abs and sdAbs. We demonstrate that even though sdAbs have smaller paratopes, they target epitopes of equal size to those targeted by Abs. To achieve this, the paratopes of sdAbs contribute more interactions per residue than the paratopes of Abs. Additionally, we find that conserved framework residues are of increased importance in the paratopes of sdAbs, suggesting that they include non-specific interactions to achieve comparable affinity. Furthermore, the epitopes of sdAbs are only marginally less accessible than those of Abs: we posit that this may be explained by differences in the orientation and compaction of sdAb and Ab CDR-H3 loops. Overall, our results have important implications for the engineering and humanization of sdAbs, as well as the selection of the best modality for targeting a particular epitope.
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