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"
Creators: name: Shcherbinin, Dmitrii S.
name: Karnaukhov, Vadim K.
name: Zvyagin, Ivan V.
name: Chudakov, Dmitriy M.
name: Shugay, Mikhail
Publisher: name: Zenodo
Year: 2023
Subjects: TCR-pMHC, VDJdb

description: <strong>Models_VDJdb.tar.gz</strong>: 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" <strong>VDJdb_Models_annotation_w_new_names.csv</strong>: spreadsheet containing annotations of the modeled structures. The following column names are used: <em><strong>vdjdb.pdb.id</strong></em>: model name in the attached database <strong><em>cdr3.alpha</em></strong>: CDR3α amino acid sequence <strong><em>cdr3.beta</em></strong>: CDR3β amino acid sequence <em><strong>orig.alpha(/beta)</strong></em>: 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). <em><strong>vdjdb.pdb.id.from</strong></em>: PDB structure that was used as a template for the modeling <em><strong>mutation.signature:</strong></em> illustration of the introduced substitution <em><strong>pdb.id:</strong></em> the model name, used during the analysis of the discussed results in the paper. <strong>Annotation_file_NEW_MUTATOR_RUN_w_NEW_PATH_Modelled_2022: </strong>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 <strong>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: </strong>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 <strong>atomdist_* file:</strong> Contains information about the close contacting (&lt;5Å) atoms of amino acid residues from different chains of the analyzed PDB files. <strong>general_* file: </strong>Provides gene annotation of chains from the analyzed PDB files. <strong>markup_* file: </strong>Contains sequence annotation of the main parts of chains from the analyzed PDB files, including CDR loops, FR-regions, and other relevant information. <strong>resmarkup_* file: </strong>Provides per-residue sequence annotation of the main parts of chains from the analyzed PDB files, including CDR loops, FR-regions, and other relevant information. <strong>NEW_MUTATOR_RUN_w_NEW_PATH_Modelled_2022_TOTAL_SCORES, NEW_MUTATOR_RUN_w_NEW_PATH_Modelled_2022_BYRES_SCORES: </strong>The files contain total or per-residue interface energy values, accompanied by the identification of the used scoring energy function. <strong>RIN_NEW_MUTATOR_RUN_w_NEW_PATH_Modelled_2022: </strong>The files provide annotation for the contacting parts of TCRs with peptides or MHC molecules in the modeled complexes. This annotation includes the identification of types of interactions and the specific contacting parts involved. <strong>blosum_col.csv_FULL2 : </strong>Blosum scores values <strong>neighbors.mut_v_3aa_mhc_tcr_cdr3_HM_ONLY_same_pept_sorted_2022_04.txt: </strong>The "pathways" file indicating mutations to introduce in template PDB files and their order <strong>vdjdb.slim.txt: </strong>VDJDB database <strong>Normal_pdbs_Min_energy_resid_list.csv, Normal_pdbs_Min_energy_resid_list_w_cdr3_pose.csv: </strong>The files contain calculated interface energy values for the TCR-peptide-MHC complexes obtained from the PDB databank. <strong>Original_PDB_top_impact_CDR3_pept_Poses.xlsx: </strong>The files provide the minimal values of interface energy calculated for the amino acid pairs between CDR3 loops and peptide in the original PDB templates <strong>Original_structures_w_descriptors_Art.csv: </strong>File contains calculated amino descriptors for the TCR-peptide-MHC complexes obtained from the PDB databank