Free Data for the People
For those interested in computational T-cell immunology, the VDJdb is an excellent resource for extracting information on T-cell receptors (TCRs) and their antigens.
T cells mediate many of their actions through specific interactions between T-cell receptors and (in most cases) peptide antigens bound to MHC molecules. This interaction can determine, for example, whether a cytotoxic T cell kills a target cell presenting a cancer antigen.
Much of computational immunology research deals with determining which antigens bind to specific T-cell receptor sequences, given the virtually infinite combinations of possible antigens and TCRs.
The VDJdb (named after V(D)J recombination, which generates TCRs and BCRs during development) provides curated listings of TCR and antigen combinations. The database is a valuable starting point for annotating TCR sequencing datasets or identifying candidate TCRs for specific antigens.
In summary, the VDJdb is a must-know resource for computational immunology researchers.
Data Scope
TCR sequences from human, mouse, and monkey species
40,000 human TCR sequences associated with over 1,000 unique epitopes
Options to search for sequence motifs, MHC classes, gene usage, and more
🔬 Experimental Techniques
TCR-antigen pairing data are collected from various studies and experimental techniques used to delineate specificity among TCRs, MHCs, and antigens.
These methods include multimer sorting of T cells, single-cell analysis, and in vitro stimulation.
Each method has its pros and cons, producing false positive and false negative interactions. Reported interactions should always be investigated in the context of the assay that produced the data.
⚠️ Data Accessibility
All data are freely available to download from the webpage as CSV files. This includes references to original studies, which is very helpful for validating results.
Have a look: https://vdjdb.cdr3.net/
👉 Do you need support navigating the VDJdb or curating public data for your research project? EVOBYTE Digital Biology is here to support you.