Reading the repertoire: Progress in adaptive immune receptor analysis using machine learning

TJ O'Donnell, C Kanduri, G Isacchini, JP Limenitakis… - Cell Systems, 2024 - cell.com
The adaptive immune system holds invaluable information on past and present immune
responses in the form of B and T cell receptor sequences, but we are limited in our ability to …

TCR3d 2.0: expanding the T cell receptor structure database with new structures, tools and interactions

V Lin, M Cheung, R Gowthaman… - Nucleic Acids …, 2024 - academic.oup.com
Recognition of antigens by T cell receptors (TCRs) is a key component of adaptive immunity.
Understanding the structures of these TCR interactions provides major insights into immune …

[HTML][HTML] Strengths and limitations of web servers for the modeling of TCRpMHC complexes

HN Le, MV de Freitas, DA Antunes - Computational and Structural …, 2024 - Elsevier
Cellular immunity relies on the ability of a T-cell receptor (TCR) to recognize a peptide (p)
presented by a class I major histocompatibility complex (MHC) receptor on the surface of a …

Quantifying conformational changes in the TCR: pMHC-I binding interface

B McMaster, CJ Thorpe, J Rossjohn… - Frontiers in …, 2024 - frontiersin.org
Background T cells form one of the key pillars of adaptive immunity. Using their surface
bound T cell antigen receptors (TCRs), these cells screen millions of antigens presented by …

T-cell receptor structures and predictive models reveal comparable alpha and beta chain structural diversity despite differing genetic complexity

NP Quast, B Guloglu, B Abanades, V Karuppiah… - bioRxiv, 2024 - biorxiv.org
T-cell receptor (TCR) structures are currently under-utilised in early-stage drug discovery
and repertoire-scale informatics. Here, we leverage a large dataset of solved TCR structures …

Structural analyses of Cryptosporidium parvum epitopes reveal a novel scheme of decapeptide binding to H-2Kb

Y Wang, Y Chang, F Yin, C Kang, Y Meng, F Xu… - Journal of Structural …, 2025 - Elsevier
Cryptosporidium has gained much attention as a major cause of diarrhea worldwide. Here,
we present the first structure of H-2K b complexed with a decapeptide from Cryptosporidium …

Structural characterization and AlphaFold modeling of human T cell receptor recognition of NRAS cancer neoantigens

D Wu, R Yin, G Chen, HV Ribeiro-Filho, M Cheung… - bioRxiv, 2024 - biorxiv.org
T cell receptors (TCRs) that recognize cancer neoantigens are important for anti-cancer
immune responses and immunotherapy. Understanding the structural basis of TCR …

Infectious diseases, imposing density-dependent mortality on MHC/HLA variation, can account for balancing selection and MHC/HLA polymorphism

DPL Green - arXiv preprint arXiv:2501.00767, 2025 - arxiv.org
The human MHC transplantation loci (HLA-A,-B,-C,-DPB1,-DQB1,-DRB1) are the most
polymorphic in the human genome. It is generally accepted this polymorphism reflects a role …

[PDF][PDF] Comparative Analysis of TCR and TCR-pMHC Complex Structure Prediction Tools

Y Shi - 2024 - trace.tennessee.edu
T cell receptor (TCR) and TCR-peptide-major histocompatibility complex (pMHC) structure
prediction tools have developed rapidly following AlphaFold's success. While these deep …