TCR3d 2.0: expanding the T cell receptor structure database with new structures, tools and interactions.
Valerie Lin1,2, Melyssa Cheung2,3, Ragul Gowthaman1,2
1Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
Nucleic Acids Research
|September 27, 2024
Summary
The TCR3d database now includes expanded structural data and tools for T cell receptor (TCR) interactions, enhancing research in immunology and therapeutic design.
Area of Science:
- Immunology
- Structural Biology
- Computational Biology
Background:
- T cell receptor (TCR) recognition of antigens is central to adaptive immunity.
- Understanding TCR-antigen structures offers insights into immune responses, diseases, and therapeutic development.
- The TCR3d database previously provided structural resources for TCR recognition.
Purpose of the Study:
- To update and expand the TCR3d database with new structural data and computational tools.
- To enhance the resource for research in immunology, therapeutics, and structural biology.
- To support advanced predictive modeling and design of TCR-related interventions.
Main Methods:
- Expansion of TCR3d database content, including new tables for TCR mimic antibody complexes, TCR-CD3 complexes, and annotated peptide-MHC complexes.
- Inclusion of binding affinity data for experimentally determined TCR-peptide-MHC complexes.
- Development of user tools for calculating docking geometries of TCR and TCR mimic complex structures.
Main Results:
- Substantial growth in TCR3d content over the past five years, reflecting an increase in available structural data.
- The TCR-peptide-MHC complex tables have increased by 50%, now incorporating binding affinity data.
- New categories of complex structures and computational tools have been added, broadening the database's utility.
Conclusions:
- The enhanced TCR3d database serves as a more comprehensive resource for studying TCR interactions.
- Updates facilitate advanced research in predictive TCR modeling, therapeutic design, and vaccine development.
- TCR3d continues to be a valuable platform for the structural biology and immunology research communities.
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