ArticleScientific reports2022
Antibody CDR amino acids underlying the functionality of antibody repertoires in recognizing diverse protein antigens.
Article in Scientific reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 33 citations in OpenAlex.
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- DeepRank-Ab: a scoring function for antibody-antigen complexes based on geometric deep learning.Communications biology · 2026Article
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- In Silico Ligand-Based Screening of PDB Database for Searching Unique Motifs Against SARS-CoV-2.Biomolecules · 2026Article
- Amino Acids Frequency and Interaction Trends: Comprehensive Analysis of Experimentally Validated Viral Antigen-Antibody Complexes.Molecular biotechnology · 2026Article
- In Silico Characterization of Conserved Epitopes in Alphavirus E2 Proteins: A Promising Approach for Pan-vaccine Design.ACS omega · 2025Article
- Strategies to Screen and Evaluate Brain Targeting Antibodies Using an iPSC-Derived Blood-Brain Barrier Model.Antibodies (Basel, Switzerland) · 2025Article
- HuAbDiffusion: a discrete language diffusion model used for antibody humanization.Briefings in bioinformatics · 2025Article
- Exploring Experimental and In Silico Approaches for Antibody-Drug Conjugates in Oncology Therapies.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Advancements in antibody-drug conjugates as cancer therapeutics.Journal of the National Cancer Center · 2025Review
- Design, Construction, and Validation of a Yeast-Displayed Chemically Expanded Antibody Library.ACS synthetic biology · 2025Article
- 50 Years of Antibody Numbering Schemes: A Statistical and Structural Evaluation Reveals Key Differences and Limitations.Antibodies (Basel, Switzerland) · 2024Article
- A comparison of antibody-antigen complex sequence-to-structure prediction methods and their systematic biases.Protein science : a publication of the Protein Society · 2024Article
- A Comparison of Antibody-Antigen Complex Sequence-to-Structure Prediction Methods and their Systematic Biases.bioRxiv : the preprint server for biology · 2024Article
- Design, Construction, and Validation of a Yeast-Displayed Chemically Expanded Antibody Library.bioRxiv : the preprint server for biology · 2024Article
- Evolution of immunogenetic components encoding ultralong CDR H3.Immunogenetics · 2023Article
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Antibodies recognize protein antigens with exquisite specificity in a complex aqueous environment, where interfacial waters are an integral part of the antibody-protein complex interfaces. In this work, we elucidate, with computational analyses, the principles governing the antibodies' specificity and affinity towards their cognate protein antigens in the presence of explicit interfacial waters. Experimentally, in four model antibody-protein complexes, we compared the contributions of the interaction types in antibody-protein antigen complex interfaces with the antibody variants selected from phage-displayed synthetic antibody libraries. Evidently, the specific interactions involving a subset of aromatic CDR (complementarity determining region) residues largely form the predominant determinant underlying the specificity of the antibody-protein complexes in nature. The interfacial direct/water-mediated hydrogen bonds accompanying the CDR aromatic interactions are optimized locally but contribute little in determining the epitope location. The results provide insights into the phenomenon that natural antibodies with limited sequence and structural variations in an antibody repertoire can recognize seemingly unlimited protein antigens. Our work suggests guidelines in designing functional artificial antibody repertoires with practical applications in developing novel antibody-based therapeutics and diagnostics for treating and preventing human diseases.
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