Known specificity human TCR CDR3 sequences

The hypervariable complementarity determining region 3 (CDR3) of T-cell receptors (TCRs) forms the major contacts with the peptide-MHC molecule, and thus is the key site of determining antigen specificity. In this dataset I have gathered CDR3 sequences from the literature, in order so that we may use these to search our high-throughput TCR repertoire DNA-sequencing data. The CDR3s gathered fall into one of two categories. The first category consists of CDR3s from TCRs reported to be reactive against known viral epitopes. This category includes CDR3s specific for human immunodeficiency virus (HIV), cytomegalovirus (CMV) and Epstein-Barr virus (EBV) (the latter two virus' CDR3 lists being collated and kindly contributed by Ilgar Mamedov, see Zvyagin et al, 2014). The second category consists of CDR3s of TCRs belonging to particular subsets of T-cells that are known to make use of partially invariant TCRs, namely (invariant) natural killer T-cells (i/NKT cells), mucosal associated invariant T (MAIT) cells and germline-encoded mycolyl-lipid reactive (GEM) cells. CDR3s are presented in lists in a format to be read into Python scripts. All CDR3 papers are referenced in the file.