ArticlePLoS computational biology2021
Epitope profiling using computational structural modelling demonstrated on coronavirus-binding antibodies.
Article in PLoS computational biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 55 citations in OpenAlex.
- Structural T-Cell Receptor Analysis in the Age of Machine Learning.Immunological reviews · 2026Review
- Contrastive learning enables epitope overlap predictions for targeted antibody discovery.Patterns (New York, N.Y.) · 2026Article
- Physicochemical convergence in antibody CDR3-VH repertoires recognizing phosphorothioate-modified oligonucleotides backbone.Frontiers in immunology · 2026Article
- Optimizing the breadth of SARS-CoV-2-neutralizing antibodies in vivo and in silico.Human vaccines & immunotherapeutics · 2025Review
- STCRpy: a software suite for T-cell receptor structure parsing, interaction profiling, and machine learning dataset preparation.Bioinformatics (Oxford, England) · 2025Article
- Rapid discovery of monoclonal antibodies by microfluidics-enabled FACS of single pathogen-specific antibody-secreting cells.Nature biotechnology · 2025Article
- Comparison of sequence- and structure-based antibody clustering approaches on simulated repertoire sequencing data.PLoS computational biology · 2025Article
- T-cell receptor structures and predictive models reveal comparable alpha and beta chain structural diversity despite differing genetic complexity.Communications biology · 2025Article
- Pox-AbDab: the orthopoxvirus antibody database.Frontiers in immunology · 2025Article
- Structure-Based Epitope Profiling with the Structural Profiling of Antibodies to Cluster by Epitope 2 (SPACE2) Algorithm.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Rapid affinity optimization of an anti-TREM2 clinical lead antibody by cross-lineage immune repertoire mining.Nature communications · 2024Article
- Computational detection of antigen-specific B cell receptors following immunization.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- NanoBERTa-ASP: predicting nanobody paratope based on a pretrained RoBERTa model.BMC bioinformatics · 2024Article
- Building Representation Learning Models for Antibody Comprehension.Cold Spring Harbor perspectives in biology · 2024Review
- Contextualising the developability risk of antibodies with lambda light chains using enhanced therapeutic antibody profiling.Communications biology · 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
- Benchmarking antibody clustering methods using sequence, structural, and machine learning similarity measures for antibody discovery applications.Frontiers in molecular biosciences · 2024Article
- Insights into next generation sequencing guided antibody selection strategies.Scientific reports · 2023Article
- SARS-CoV-2 antibodies recognize 23 distinct epitopic sites on the receptor binding domain.Communications biology · 2023Article
- KA-Search, a method for rapid and exhaustive sequence identity search of known antibodies.Scientific reports · 2023Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Identifying the epitope of an antibody is a key step in understanding its function and its potential as a therapeutic. Sequence-based clonal clustering can identify antibodies with similar epitope complementarity, however, antibodies from markedly different lineages but with similar structures can engage the same epitope. We describe a novel computational method for epitope profiling based on structural modelling and clustering. Using the method, we demonstrate that sequence dissimilar but functionally similar antibodies can be found across the Coronavirus Antibody Database, with high accuracy (92% of antibodies in multiple-occupancy structural clusters bind to consistent domains). Our approach functionally links antibodies with distinct genetic lineages, species origins, and coronavirus specificities. This indicates greater convergence exists in the immune responses to coronaviruses than is suggested by sequence-based approaches. Our results show that applying structural analytics to large class-specific antibody databases will enable high confidence structure-function relationships to be drawn, yielding new opportunities to identify functional convergence hitherto missed by sequence-only analysis.
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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.