Datasets associated with the manuscript "Discovering SARS-CoV-2 neoepitopes and the associated TCR-pMHC recognition mechanisms by combining single-cell sequencing, deep learning, and molecular dynamics simulation techniques"

meta_data_TCR-pMHC_from_STCRDab.tsv, TCR-pMHC structures used for contacts analysis.
tcr_gliph_input_sars2.tsv, input files (TCR sequences and related information) used for clustering TCRs targeting SARS-CoV-2 epitopes and epitope-unknown TCRs.
tcr_gliph_input_non-sars2.tsv, input files used for clustering TCRs targeting non-SARS-CoV-2 epitopes and epitope-unknown TCRs.
tcr_gliph_output*, output files from the GLIPH software, including the recognized TCR clusters by GLIPH (convergence-group.txt), the linkage information of TCR clusters (clone-network.txt), and the recognized motif in TCR clusters (kmer.txt).
md_trajs.tar, structures and MD simulation trajectories of TCR-614-pMHC and TCR-204-pMHC complexes.