ArticleNucleic acids research2015
LYRA, a webserver for lymphocyte receptor structural modeling.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed, 93 citations in OpenAlex.
- Structural Basis for Clonal Diversity of the Public T Cell Response to a Dominant Human Cytomegalovirus Epitope.The Journal of biological chemistry · 2015Trial
- Structural T-Cell Receptor Analysis in the Age of Machine Learning.Immunological reviews · 2026Review
- Mapping the TCR landscape: computational tools empowering translational immunology and therapy design.Journal for immunotherapy of cancer · 2026Review
- SwiftTCR: efficient computational docking protocol of TCRpMHC-I complexes using restricted rotation matrices.Briefings in bioinformatics · 2026Article
- AI-powered mapping of tumor immunity for optimized mRNA vaccine engineering.Frontiers in oncology · 2026Review
- Article
- Structural quality-tier assessment for TCR-pMHC functional enrichment.Frontiers in immunology · 2026Article
- AbEpiTope-1.0: Improved antibody target prediction by use of AlphaFold and inverse folding.Science advances · 2025Article
- TRain: T-cell receptor automated immunoinformatics.BMC bioinformatics · 2025Article
- T-cell receptor structures and predictive models reveal comparable alpha and beta chain structural diversity despite differing genetic complexity.Communications biology · 2025Article
- A fingerprint approach to pioneer structure-based T cell receptor repertoire analysis and specificity prediction.Frontiers in immunology · 2025Article
- A Computational Strategy for the Rapid Identification and Ranking of Patient-Specific T Cell Receptors Bound to Neoantigens.Macromolecular rapid communications · 2024Article
- Strengths and limitations of web servers for the modeling of TCRpMHC complexes.Computational and structural biotechnology journal · 2024Article
- Article
- Identification of Conserved Linear Epitopes on Viral Protein 2 of Foot-and-Mouth Disease Virus Serotype O by Monoclonal Antibodies 6F4.D11.B6 and 8D6.B9.C3.Antibodies (Basel, Switzerland) · 2024Article
- Next-generation IEDB tools: a platform for epitope prediction and analysis.Nucleic acids research · 2024Article
- Can AlphaFold's breakthrough in protein structure help decode the fundamental principles of adaptive cellular immunity?Nature methods · 2024Review
- Single-residue linear and conformational B cell epitopes prediction using random and ESM-2 based projections.Briefings in bioinformatics · 2024Article
- Computational biology and artificial intelligence in mRNA vaccine design for cancer immunotherapy.Frontiers in cellular and infection microbiology · 2024Review
- Multi-perspectives and challenges in identifying B-cell epitopes.Protein science : a publication of the Protein Society · 2023Review
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
The accurate structural modeling of B- and T-cell receptors is fundamental to gain a detailed insight in the mechanisms underlying immunity and in developing new drugs and therapies. The LYRA (LYmphocyte Receptor Automated modeling) web server (http://www.cbs.dtu.dk/services/LYRA/) implements a complete and automated method for building of B- and T-cell receptor structural models starting from their amino acid sequence alone. The webserver is freely available and easy to use for non-specialists. Upon submission, LYRA automatically generates alignments using ad hoc profiles, predicts the structural class of each hypervariable loop, selects the best templates in an automatic fashion, and provides within minutes a complete 3D model that can be downloaded or inspected online. Experienced users can manually select or exclude template structures according to case specific information. LYRA is based on the canonical structure method, that in the last 30 years has been successfully used to generate antibody models of high accuracy, and in our benchmarks this approach proves to achieve similarly good results on TCR modeling, with a benchmarked average RMSD accuracy of 1.29 and 1.48 Å for B- and T-cell receptors, respectively. To the best of our knowledge, LYRA is the first automated server for the prediction of TCR structure.
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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.