ArticlemAbs
Length-independent structural similarities enrich the antibody CDR canonical class model.
Article in mAbs. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 61 citations in OpenAlex.
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- T-cell receptor structures and predictive models reveal comparable alpha and beta chain structural diversity despite differing genetic complexity.Communications biology · 2025Article
- Antibody numbering schemes: advances, comparisons and tools for antibody engineering.Protein engineering, design & selection : PEDS · 2025Review
- 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
- Antigen binding triggers long-range conformational changes in monoclonal antibodies.Frontiers in immunology · 2025Article
- TPepRet: a deep learning model for characterizing T-cell receptors-antigen binding patterns.Bioinformatics (Oxford, England) · 2024Article
- Investigating the ability of deep learning-based structure prediction to extrapolate and/or enrich the set of antibody CDR canonical forms.Frontiers in immunology · 2024Article
- Structural mechanism of Fab domain dissociation as a measure of interface stability.Journal of computer-aided molecular design · 2023Article
- Specific attributes of the VFrontiers in immunology · 2023Article
- Improved computational epitope profiling using structural models identifies a broader diversity of antibodies that bind to the same epitope.Frontiers in molecular biosciences · 2023Article
- Structural modeling of antibody variable regions using deep learning-progress and perspectives on drug discovery.Frontiers in molecular biosciences · 2023Review
- Structure-Based Optimization of Antibody-Based Biotherapeutics for Improved Developability: A Practical Guide for Molecular Modelers.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Computational identification of HCV neutralizing antibodies with a common HCDR3 disulfide bond motif in the antibody repertoires of infected individuals.Nature communications · 2022Review
- A novel framework for engineering protein loops exploring length and compositional variation.Scientific reports · 2021Article
- Discovery of Marburg virus neutralizing antibodies from virus-naïve human antibody repertoires using large-scale structural predictions.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Antibodies exhibit multiple paratope states influencing VCommunications biology · 2020Article
- How repertoire data are changing antibody science.The Journal of biological chemistry · 2020Review
- Structural diversity of B-cell receptor repertoires along the B-cell differentiation axis in humans and mice.PLoS computational biology · 2020Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Complementarity-determining regions (CDRs) are antibody loops that make up the antigen binding site. Here, we show that all CDR types have structurally similar loops of different lengths. Based on these findings, we created length-independent canonical classes for the non-H3 CDRs. Our length variable structural clusters show strong sequence patterns suggesting either that they evolved from the same original structure or result from some form of convergence. We find that our length-independent method not only clusters a larger number of CDRs, but also predicts canonical class from sequence better than the standard length-dependent approach. To demonstrate the usefulness of our findings, we predicted cluster membership of CDR-L3 sequences from 3 next-generation sequencing datasets of the antibody repertoire (over 1,000,000 sequences). Using the length-independent clusters, we can structurally classify an additional 135,000 sequences, which represents a ∼20% improvement over the standard approach. This suggests that our length-independent canonical classes might be a highly prevalent feature of antibody space, and could substantially improve our ability to accurately predict the structure of novel CDRs identified by next-generation sequencing.
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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.