| --- |
| license: cc-by-nc-nd-4.0 |
| tags: |
| - tcr |
| - epitope |
| - antigen |
| - mhc |
| - hla |
| - t-cell |
| - receptor |
| - structure |
| - pdb |
| - complex |
| - binding |
| pretty_name: vdjdb_structures |
| --- |
| |
| ## Predicted structures for VDJdb records |
|
|
| This repository contains structure data for selected VDJdb records obtained using AI-based modelling in `data/` folder: |
| * `pdb_files.tgz` contains predicted TCR:pMHC structures with canonical chain names, orientation and placement, superimposed by aligning and rotation. File names start with `tcr_pmhc_hash` which must be used for connecting the structure with the VDJdb record. |
| * `pdb_files_native.tgz` contains real TCR:pMHC structures from PDB, processed to canonical coordinated in the same way as `pdb_files.tgz`. |
| * `coordinates_aa.tgz` contains tables with amino acid Ca atom coordinates for each residue of deposited structures. |
| * `contacts_aa.tgz` contains files with residue pairs at a distance <= 5A for each of the deposited structures. Currently only TCR alpha CDR3-peptide and beta CDR3-peptide are considered. |
| * `complementarity_maps.tgz` and `complementarity_maps_simplified.tgz` contains 2D projections of TCR alpha CDR3, TCR beta CDR3 and peptide residue coordinates in for of SVG plots produced by matplotlib. |
|
|
| Metadata for all structures is concatenated with corresponding VDJdb record metadata and stored in `vdjdb_structures_metadata.tsv.gz`. The file contains default VDJdb "full table" columns together with the following columns calculated for each structure: |
| * `num_contacts` - number of contacts in the available structure between TCR and peptide. |
| * `ranking_confidence`, `plddt`, `ptm`, `iptm`, `tcr_pmhc_iptm` - TCRmodel2 quality metrics (for more information please visit [TCRmodel2 webpage](https://tcrmodel.ibbr.umd.edu/help)). |
| * `scanning_angle` and `pitch_angle` - scanning and pitch TCR:pMHC structure angles calculated with STCRpy. |
| * `is_native` - whether the structure is experimentally acquired (from PDB) or predicted. |
| * `tcr_pmhc_hash` - unique TCR:pMHC record hash for matching predicted structure PDBs. |
