---
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.

## Contents at a glance

| | |
|---|---|
| metadata rows | 15,018 (11,234 distinct `tcr_pmhc_hash`) |
| predicted / native rows | 14,612 / 406 |
| PDB files shipped | 10,884 predicted (`pdb_files.tgz`) + 369 native (`pdb_files_native.tgz`) |
| epitopes / MHC alleles | 249 / 81 |
| MHC class | 14,915 MHC-I, 103 MHC-II |
| species | 14,928 human, 90 mouse |

A metadata row without a matching PDB is normal — the file set is the subset that modelled and passed
QC. Join on `tcr_pmhc_hash`; predicted filenames are `aligned_aligned_<hash>.pdb`, natives are
`aligned_<pdbid>.pdb`.

## Provenance

- **TCR:epitope pairings are EXPERIMENTAL** — VDJdb records, carried through with the full VDJdb
  "full table" columns (`reference.id`, `method.*`, `meta.*`, `vdjdb.score`).
- **Predicted structures are COMPUTED** (TCRmodel2/AlphaFold). `ranking_confidence`, `plddt`, `ptm`,
  `iptm`, `tcr_pmhc_iptm` are the generator's own confidence metrics, not measurements.
- **Native structures are EXPERIMENTAL** (RCSB), re-processed into the same canonical frame.
- **Derived columns** (`num_contacts`, `scanning_angle`, `pitch_angle`) are computed from the
  deposited coordinates — for predicted rows they inherit the model's error, and the angles in
  particular track AlphaFold confidence rather than being independent of it.

## Used by

The TCRen2 receptor-ranking benchmark (`isalgo/tcren_structures`) draws its **real-binder positives**
from this pool — filtered to `is_native == False`, restricted to hashes present in `pdb_files.tgz`,
and with TCRvdb pairs excluded — then matches them per epitope against the decoys in
`isalgo/tcren_structures::vdjdb_negatives/` and `::immrep23_negatives/`. See
`isalgo/tcren_structures::vdjdb_binder_benchmark/README.md`.