ArticleThe Journal of biological chemistry2025
Evaluation of AlphaFold modeling for elucidation of nanobody-peptide epitope interactions.
Article in The Journal of biological chemistry, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Multivalent antibody-based conjugates as new tools for tailored modulation of G protein-coupled receptors.British journal of pharmacology · 2026Review
- Benchmarking AlphaFold and related deep learning approaches for modeling antibody and TCR antigen recognition.bioRxiv : the preprint server for biology · 2026Article
- Benchmarking all-atom biomolecular structure prediction with FoldBench.Nature communications · 2025Article
- Development of bitopic nanobody-ligand conjugates targeting G protein-coupled receptors and exhibiting logic-gated signaling.PLoS biology · 2025Article
- Computational nanobody design through deep generative modeling and epitope landscape profiling.Computational and structural biotechnology journal · 2025Article
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10 authors.
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Abstract
Models of antibody (Ab)-antigen complexes can be used to understand interaction mechanisms and for improving affinity. This study evaluates the use of the protein structure prediction algorithm AlphaFold (AF) for exploration of interactions between peptide epitope tags and the smallest functional Ab fragments, nanobodies (Nbs). Although past studies of AF for modeling Ab-target (antigen) interactions suggested modest algorithm performance, those were primarily focused on Ab-protein interactions, while the performance and utility of AF for Nb-peptide interactions, which are generally less complex because of smaller antigens, smaller binding domains, and fewer chains, is less clear. In this study, we evaluated the performance of AF for predicting the structures of Nbs bound to experimentally validated, linear, short peptide epitopes (Nb-tag pairs). We expanded the pool of experimental data available for comparison through crystallization and structural determination of a previously reported Nb-tag complex (Nb
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