Frequently Asked Questions
Where are the structures from?These TCR structures are experimentally determined x-ray structures from the Protein Data Bank. We search the PDB for TCR structures using hidden markov models (HMMs) built from TCR alpha and beta variable domain sequences, and structures of TCRs identified from this search are downloaded, analyzed for various structural and docking features, and curated to remove extraneous domains, chains, and non-protein atoms, in order to facilitate user visualization and analysis.
What are crossing angle and incident angle, and how are they calculated?
They correspond to the TCR twist and tilt with respect to the peptide-MHC in the bound complex. More information can be found here.
How are the buried surface area (BSA) calculated?
The BSA is calculated using the program Naccess (Version 2.1.1). The default probe size of 1.40 Å is used and all HETATM records, hydrogens, and waters were excluded in the calculation.
Whom should I contact with questions or suggestions?
Brian Pierce. This site was developed by the Pierce Lab.
How do I cite the database?
Please see this reference (PMID: 31240309) and cite it if you use the database in your work:
Ragul Gowthaman, Brian G Pierce, TCR3d: The T cell receptor structural repertoire database, Bioinformatics, , btz517, https://doi.org/10.1093/bioinformatics/btz517