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README.md

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+## Predicted structures for VDJdb records
+
+This repository contains structure data for selected VDJdb records obtained using AI-based modelling:
+* The folder `pdb_files` 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.
+* The folder `pdb_files_native` contains real TCR:pMHC structures from PDB, processed to canonical coordinated in the same way as `pdb_files`.
+* The folder `coordinates_aa` contains tables with amino acid Ca atom coordinates for each residue of deposited structures.
+* The folder `contacts_aa` 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.
+* The folder `contact_maps` 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.  

vdjdb_structures_metadata.tsv.gz

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