Monthly Archives: February 2018

TCR Database

Back-to-back posting – I wanted to talk about the growing volume of TCR structures in the PDB. A couple of weeks ago, I presented my database to the group (STCRDab), which is now available at http://opig.stats.ox.ac.uk/webapps/stcrdab.

Unlike other databases, STCRDab is fully automated and updates on Fridays at 9AM (GMT), downloading new TCR structures and annotating them with the IMGT numbering (also applies for MHCs!). Although the size of the data is significantly smaller than, say, the number of antibody structures (currently at 3000+ structures and growing), the recent approval of CAR therapies (Kymriah, Yescarta), and the rise of interest in TCR engineering (e.g. Glanville et al., Nature, 2017; Dash et al., Nature, 2017) point toward the value of structures.

Feel free to read more in the paper, and here are some screenshots. 🙂

STCRDab front page.

Look! 5men, literally.

Possibly my new favourite PDB code.

STCRDab annotates structures automatically every Friday!

ABodyBuilder and model quality

Currently I’m working on developing a new strategy to use FREAD within the ABodyBuilder pipeline. While running some tests I’ve realised that some of the RMSD values that there were some minor miscalculations of CDR loops’ RMSD in my paper.

To start with, the main message of the paper remains the same; the overall quality of the models (Fv RMSD) was correct, and still is. ABodyBuilder isn’t necessarily the most accurate modelling methodology per se, but it’s unique in its ability to estimate RMSD. ABodyBuilder would still be capable of doing this calculation regardless of what the CDR loops’ RMSD may be. This is because the accuracy estimation looks at the RMSD data and places a probability that a new model structure would have some RMSD value “x” (given the CDR loop’s length). Our website has now been updated in light of these changes too.

Update to Figure 2 of the paper.

Update to Figure S4 of the paper.

Update to Figure S5 of the paper.