ArticleComputational and structural biotechnology journal2024
Structural trends in antibody-antigen binding interfaces: a computational analysis of 1833 experimentally determined 3D structures.
Article in Computational and structural biotechnology journal, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 32 citations in OpenAlex.
- Mass spectrometry-based mapping of conformational epitopes on SARS-CoV-2 antigens targeted by monoclonal antibodies.International journal of biological macromolecules · 2026Article
- Epitope-Imprinted Polymers for Selective Recognition of Bacterial Proteins: From Design to Analytical Applications.ACS measurement science au · 2026Review
- Highly potent C-type nanoantibodies neutralize Nipah and Hendra viruses by cavity filling on fusion glycoprotein.Nature communications · 2026Article
- Decoding epitope immunodominance in HIV Env using cryoEM and machine learning.bioRxiv : the preprint server for biology · 2026Article
- Integrating deep learning with physics based modeling enables high precision antibody antigen interface prediction.Scientific reports · 2026Article
- Phosphorylation of a Tumor-Derived ASXL2 Epitope Remodels the HLA-Bound Peptide Conformational Ensemble and Interaction Network of the Peptide-HLA Complex.Computational and structural biotechnology journal · 2026Article
- Article
- Revisiting the Ofatumumab Epitope on CD20 through Integrative Molecular Dynamics and Flow Cytometry Analyses.Computational and structural biotechnology journal · 2026Article
- Benchmarking antibody modeling tools across structure prediction, docking, and paratope-epitope interface analysis.Bioinformatics advances · 2026Article
- Ensemble molecular mimicry correlates with antibody cross-reactivity in proteome-wide studies.Frontiers in immunology · 2026Article
- High-throughput single-cell analysis reveals Omp38-specific monoclonal antibodies that protect againstEmerging microbes & infections · 2025Article
- Germline-aware deep learning models and benchmarks for predicting antibody VH-VL pairing.mAbs · 2025Article
- AbAgym: a well-curated dataset for the mutational analysis of antibody-antigen complexes.mAbs · 2025Article
- Article
- Structural and epitope characterization of anti-DEFA5 monoclonal antibodies clones 1A8 and 4F5 for inflammatory bowel disease subtype diagnostics.International journal of biological macromolecules · 2025Article
- Engineering antibody-drug conjugates targeting an adhesion GPCR, CD97.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- High-throughput single-cell analysis reveals fully human Omp38-specific monoclonal antibodies against Acinetobacter baumannii.BMC microbiology · 2025Article
- An iterative strategy to design 4-1BB agonist nanobodies de novo with generative AI models.Scientific reports · 2025Article
- Mass Spectrometry-Driven Epitope Mapping: Application of Diethylpyrocarbonate Covalent Labeling for the Immunotherapeutic Target Programmed Cell Death Protein 1.Journal of the American Society for Mass Spectrometry · 2025Article
- Evaluation of AlphaFold modeling for elucidation of nanobody-peptide epitope interactions.The Journal of biological chemistry · 2025Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Antibodies are attractive therapeutic candidates due to their ability to bind cognate antigens with high affinity and specificity. Still, the underlying molecular rules governing the antibody-antigen interface remain poorly understood, making in silico antibody design inherently difficult and keeping the discovery and design of novel antibodies a costly and laborious process. This study investigates the characteristics of antibody-antigen binding interfaces through a computational analysis of more than 850,000 atom-atom contacts from the largest reported set of antibody-antigen complexes with 1833 nonredundant, experimentally determined structures. The analysis compares binding characteristics of conventional antibodies and single-domain antibodies (sdAbs) targeting both protein- and peptide antigens. We find clear patterns in the number antibody-antigen contacts and amino acid frequencies in the paratope. The direct comparison of sdAbs and conventional antibodies helps elucidate the mechanisms employed by sdAbs to compensate for their smaller size and the fact that they harbor only half the number of complementarity-determining regions compared to conventional antibodies. Furthermore, we pinpoint antibody interface hotspot residues that are often found at the binding interface and the amino acid frequencies at these positions. These findings have direct potential applications in antibody engineering and the design of improved antibody libraries.
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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 Socratic graph.