ArticleMolecular immunology2013
Structural analysis of B-cell epitopes in antibody:protein complexes.
Article in Molecular immunology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 155 papers.
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Who cites it
155 citing papers in PubMed, 305 citations in OpenAlex.
- Multi-dimensional orchestration of binders for improved CAR-T immunotherapy.Cancer letters · 2026Review
- Proteome-wide characterization of Plasmodium vivax antigens using a high-density peptide array.PLoS pathogens · 2026Article
- PatchEpi: patch-aware equivariant learning improves structure-based epitope prediction.Bioinformatics (Oxford, England) · 2026Article
- Reconstructing pathogen-specific antibody binding epitopes and age-dependent immune signatures from proteomic-scale peptide libraries.Science advances · 2026Article
- In silico design and evaluation of a candidate multiepitope Salmonella vaccine construct targeting broad-spectrum protection in poultry.BMC genomics · 2026Article
- IgM and IgG Epitope Mapping of the Porin Outer Membrane Protein-2a fromInternational journal of molecular sciences · 2026Article
- Structural and immunogenic evaluation of silk proteins from Bombyx mori using advanced bioinformatics and deep learning for biomaterials applications.Journal, genetic engineering & biotechnology · 2026Article
- Comparison of a recombinant endonuclease III protein and its synthetic peptides in ELISA for the diagnosis of tegumentary leishmaniasis using human serum and urine samples: A preliminary study.PLoS neglected tropical diseases · 2026Article
- Dynamic changes in serum HER2-peptide-specific autoantibodies predict response to neoadjuvant therapy in HER2-positive breast cancer.Breast cancer research : BCR · 2026Article
- Convergent strategies for nanobody-mediated inhibition of an epoxide hydrolase.bioRxiv : the preprint server for biology · 2026Article
- Immunoinformatic-based design of a multi-epitope subunit vaccine against Ruminococcus torques using subtractive proteomics and molecular dynamics simulations.Scientific reports · 2026Article
- RoBep: a region-oriented deep learning model for B-cell epitope prediction.Bioinformatics (Oxford, England) · 2026Article
- Amino Acids Frequency and Interaction Trends: Comprehensive Analysis of Experimentally Validated Viral Antigen-Antibody Complexes.Molecular biotechnology · 2026Article
- Hepatitis C virus E1 protein-specific linear B-cell epitopes, pan-genotype reactivity, and functional relevance.Frontiers in immunology · 2026Article
- AI-powered mapping of tumor immunity for optimized mRNA vaccine engineering.Frontiers in oncology · 2026Review
- EMoMiS: A pipeline for epitope-based molecular mimicry search in protein structures with potential applications to SARS-CoV-2.Computational and structural biotechnology journal · 2026Article
- Computational Methods in Immunoinformatics: Epitope Discovery and Diagnostic Applications.ACS omega · 2025Review
- Targets of the human antibody response to the variant surface glycoprotein ofbioRxiv : the preprint server for biology · 2025Article
- Reconstructing pathogen-specific antibody binding epitopes and age-dependent immune signatures from proteomic-scale peptide libraries.medRxiv : the preprint server for health sciences · 2025Article
- Deep learning in next-generation vaccine development for infectious diseases.Molecular therapy. Nucleic acids · 2025Review
95 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
The binding of antigens to antibodies is one of the key events in an immune response against foreign molecules and is a critical element of several biomedical applications including vaccines and immunotherapeutics. For development of such applications, the identification of antibody binding sites (B-cell epitopes) is essential. However experimental epitope mapping is highly cost-intensive and computer-aided methods do in general have moderate performance. One major reason for this moderate performance is an incomplete understanding of what characterizes an epitope. To fill this gap, we here developed a novel framework for comparing and superimposing B-cell epitopes and applied it on a dataset of 107 non-similar antigen:antibody structures extracted from the PDB database. With the presented framework, we were able to describe the general B-cell epitope as a flat, oblong, oval shaped volume consisting of predominantly hydrophobic amino acids in the center flanked by charged residues. The average epitope was found to be made up of ∼15 residues with one linear stretch of 5 or more residues constituting more than half of the epitope size. Furthermore, the epitope area is predominantly constrained to a plane above the antibody tip, in which the epitope is orientated in a -30° to 60° angle relative to the light to heavy chain antibody direction. Contrary to previously findings, we did not find a significant deviation between the amino acid composition in epitopes and the composition of equally exposed parts of the antigen surface. Our results, in combination with previously findings, give a detailed picture of the B-cell epitope that may be used in development of improved B-cell prediction methods.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.