ReviewNature methods2024
Can AlphaFold's breakthrough in protein structure help decode the fundamental principles of adaptive cellular immunity?
Review in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Structure-based TCR-pMHC binding prediction and generalization to unseen peptides.npj drug discovery · 2026Article
- Benchmarking AlphaFold and related deep learning approaches for modeling antibody and TCR antigen recognition.bioRxiv : the preprint server for biology · 2026Article
- A comparative and exploratory analysis of computational methods for TCR structural prediction and antigen-specific TCR discovery.Briefings in bioinformatics · 2026Article
- Modeling TCR-Epitope Recognition Specificity: What We Should Learn to Succeed.Immunological reviews · 2026Review
- General prediction of T cell receptor antigen specificity from sequence using AlphaFold 3.bioRxiv : the preprint server for biology · 2026Article
- More protein-ligand data are needed for AlphaFold-like models to enable drug discovery.Current opinion in structural biology · 2026Review
- Benchmarking TCR-pMHC structure prediction: a unified evaluation and CDR3-based functional insights.Briefings in bioinformatics · 2026Article
- Ex Vivo Expansion of Melanoma Tumor-Infiltrating Lymphocytes Leads to a Dominant Exhausted T-cell Population with a Lack of Memory Markers.Cancer immunology research · 2026Article
- Advances in predicting T cell epitope recognition for cancer immunotherapy.Nature cancer · 2026Review
- Multimodal learning on heterogeneous subgraphs and LLMs representation for MHC-peptide binding affinity prediction.BMC bioinformatics · 2026Article
- Re: Qi et al. "A roadmap for T cell receptor-peptide-MHC binding prediction by machine learning: glimpse and foresight" (Briefings in Bioinformatics, 2025).Briefings in bioinformatics · 2026Article
- Could artificial intelligence gradually replace classical adjuvants?Frontiers in immunology · 2026Review
- Structural quality-tier assessment for TCR-pMHC functional enrichment.Frontiers in immunology · 2026Article
- Conformational Dynamics of the Active Site Loop in Dihydroorotase Highlighting the Limitations of Loop-In Structures for Inhibitor Docking.International journal of molecular sciences · 2025Article
- Identification of T-Cell Epitopes and Vaccine Development for African Swine Fever Virus.Vaccines · 2025Review
- T cell receptor cross-reactivity prediction improved by a comprehensive mutational scan database.Cell systems · 2025Article
- Identifying T cell antigen at the atomic level with graph convolutional network.Nature communications · 2025Article
- Cellular mechanical memory: a potential tool for mesenchymal stem cell-based therapy.Stem cell research & therapy · 2025Review
- T-cell receptor structures and predictive models reveal comparable alpha and beta chain structural diversity despite differing genetic complexity.Communications biology · 2025Article
- Comprehensive epitope mutational scan database enables accurate T cell receptor cross-reactivity prediction.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
T cells are essential immune cells responsible for identifying and eliminating pathogens. Through interactions between their T-cell antigen receptors (TCRs) and antigens presented by major histocompatibility complex molecules (MHCs) or MHC-like molecules, T cells discriminate foreign and self peptides. Determining the fundamental principles that govern these interactions has important implications in numerous medical contexts. However, reconstructing a map between T cells and their antagonist antigens remains an open challenge for the field of immunology, and success of in silico reconstructions of this relationship has remained incremental. In this Perspective, we discuss the role that new state-of-the-art deep-learning models for predicting protein structure may play in resolving some of the unanswered questions the field faces linking TCR and peptide-MHC properties to T-cell specificity. We provide a comprehensive overview of structural databases and the evolution of predictive models, and highlight the breakthrough AlphaFold provided the field.
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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.