As always, a huge thanks go to @mraybould.bsky.social and Charlotte Deane, as well as the the rest of @opig.stats.ox.ac.uk for the support and platform to do impactful research.
The protocol we used to develop and evaluate our structural hypothesis is described in detail in the methods, and we published the computational tool used to analyse and score TCR-antigen complexes in Bioinformatics earlier this year.
doi.org/10.1093/bioi...
This was a test whether the ML methods we develop can be used to explain molecular interactions when we have the experimental data. We used a hybrid deep-learning and physics-simulation approach to identify a structural hypothesis for the specific binding of the KRAS G12V antigen by the TCR.
I'm really pleased that our collaboration with Shira Sagie, Tomer Babu and Yardena Samuels has been published in Cell Reports Medicine. This has been a really fun and productive collaboration as well as an incredible learning process.
www.cell.com/cell-reports...
STCRpy, an easy-to-use python package for T-cell receptor structures has just been published in Bioinformatics! Big thanks to @mraybould.bsky.social and Charlotte Deane for their support, and to @opig.stats.ox.ac.uk for being an amazing collaborative group!
Paper: doi.org/10.1093/bioi...
We won the Boltz Hackathon Challenge improving computational efficiency! Big thanks to Boltz team and @merckgroup.bsky.social for the event and very proud of our prototype Boltz Flow Matching model. Huge thanks to Niklas Abraham and Aaron Schöne for being excellent collaborators! ms.spr.ly/6043tBeAL
We are looking forward to community contributions as more TCR structure research is conducted. We have also written some developer guidelines; if you have any questions just reach out!
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Big thanks to my supervisors Charlotte Deane and @mraybould.bsky.social for their supervision creating STCRpy. And all @opig.stats.ox.ac.uk for being such a fab group to be part of!
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Do you wish working with T-cell receptor structures was easier?
Us too!
STCRpy, our software suite for T cell receptor structure parsing, interaction profiling and machine learning dataset preparation is now available!
Github: github.com/npqst/stcrpy/
Pre-print: www.biorxiv.org/content/10.1...
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Applications are now open for UNIQ+ @ox.ac.uk (deadline Wed 19 February 2025)!
We're delighted to be offering a project on Nanobody Language Modelling. Learn about deep learning and language modelling and gain experience applying these methods to nanobody sequences
www.ox.ac.uk/admissions/g...
OPIG is now on Bluesky!
Follow us for updates about the group's latest work, web app updates, and more.
opig.stats.ox.ac.uk
