The database of TCR-peptide-MHC modeled structures from the paper: "Large-scale template-based structural modeling of T-cell receptors with known antigen specificity reveals complementarity features"

Models_VDJdb.tar.gz: contains TCR-peptide-MHCI modeld structures and 29 templates, discussed in the paper "Large-scale template-based structural modeling of T-cell receptors with known antigen specificity reveals complementarity features" VDJdb_Models_annotation_w_new_names.csv: spreadsheet containing annotations of the modeled structures. The following column names are used: vdjdb.pdb.id: model name in the attached database cdr3.alpha: CDR3α amino acid sequence cdr3.beta: CDR3β amino acid sequence orig.alpha(/beta): if “TRUE”, the CDR3α/β sequence is the same as in the corresponding original PDB template. If “FALSE”, the CDR3α/β carries one amino acid substitution (illustrated in the mutation.signature column). vdjdb.pdb.id.from: PDB structure that was used as a template for the modeling mutation.signature: illustration of the introduced substitution pdb.id: the model name, used during the analysis of the discussed results in the paper. Annotation_file_NEW_MUTATOR_RUN_w_NEW_PATH_Modelled_2022: The file contains annotation information for all the modeled structures, including structure names, modifications of CDR3 sequences, introduced substitutions, mutation order, and the original PDB templates atomdist_NEW_MUTATOR_RUN_w_NEW_PATH_Modelled_2022.txt (tar.gz), general_NEW_MUTATOR_RUN_w_NEW_PATH_Modelled_2022_MOD.txt, markup_NEW_MUTATOR_RUN_w_NEW_PATH_Modelled_2022.txt, resmarkup_NEW_MUTATOR_RUN_w_NEW_PATH_Modelled_2022.txt: The output files collected after running our in-house TCR-peptide-MHC complex structure annotation script, mir-1.0-SNAPSHOT.jar. You can find the script at the following GitHub repositories: https://github.com/antigenomics/mir , https://github.com/antigenomics/tcren-ms/blob/master/TCRen_pipeline/mir-1.0-SNAPSHOT.jar atomdist_* file: Contains information about the close contacting (