ArticleProteins2017
The H3 loop of antibodies shows unique structural characteristics.
Article in Proteins, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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Who cites it
68 citing papers in PubMed.
- Structural T-Cell Receptor Analysis in the Age of Machine Learning.Immunological reviews · 2026Review
- H3BERTa: A CDR-H3-specific language model for antibody repertoire analysis.Patterns (New York, N.Y.) · 2026Article
- DeepRank-Ab: a scoring function for antibody-antigen complexes based on geometric deep learning.Communications biology · 2026Article
- ANARCII enables alignment-free antigen receptor numbering using a generalised language model.Communications biology · 2026Article
- Antibody Affinity Maturation by Computational Design.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Comparison of sequence- and structure-based antibody clustering approaches on simulated repertoire sequencing data.PLoS computational biology · 2025Article
- Protein sequence modelling with Bayesian flow networks.Nature communications · 2025Article
- T-cell receptor structures and predictive models reveal comparable alpha and beta chain structural diversity despite differing genetic complexity.Communications biology · 2025Article
- AntiFold: improved structure-based antibody design using inverse folding.Bioinformatics advances · 2025Article
- Improved prediction of antibody and their complexes with clustered generative modelling ensembles.Bioinformatics advances · 2025Article
- Applying computational protein design to therapeutic antibody discovery - current state and perspectives.Frontiers in immunology · 2025Review
- Integrating In Silico and In Vitro Tools for Optimized Antibody Development-Design of Therapeutic Anti-oxMIF Antibodies.Antibodies (Basel, Switzerland) · 2024Article
- Large scale paired antibody language models.PLoS computational biology · 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
- Protein loop structure prediction by community-based deep learning and its application to antibody CDR H3 loop modeling.PLoS computational 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
- 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
- Structure and Dynamics Guiding Design of Antibody Therapeutics and Vaccines.Antibodies (Basel, Switzerland) · 2023Review
- SARS-CoV-2 antibodies recognize 23 distinct epitopic sites on the receptor binding domain.Communications biology · 2023Article
8 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The H3 loop in the Complementarity Determining Region of antibodies plays a key role in their ability to bind the diverse space of potential antigens. It is also exceptionally difficult to model computationally causing a significant hurdle for in silico development of antibody biotherapeutics. In this article, we show that most H3s have unique structural characteristics which may explain why they are so challenging to model. We found that over 75% of H3 loops do not have a sub-Angstrom structural neighbor in the non-antibody world. Also, in a comparison with a nonredundant set of all protein fragments over 30% of H3 loops have a unique structure, with the average for all of other loops being less than 3%. We further observed that this structural difference can be seen at the level of four residue fragments where H3 loops present numerous novel conformations, and also at the level of individual residues with Tyrosine and Glycine often found in energetically unfavorable conformations. Proteins 2017; 85:1311-1318. © 2017 Wiley Periodicals, Inc.
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