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Benjie McMaster @benjamin-mcmaster.bsky.social · 20/07/2026

A big thank you to my co-authors: Ali El Moselhy, Ili Ilievski, Christopher Thorpe, Nicole La Gruta, and Jamie Rossjohn, as well as to my supervisors Hashem and Charlotte for their support throughout.

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Benjie McMaster @benjamin-mcmaster.bsky.social · 20/07/2026

Our results demonstrate both the remarkable potential of these models for understanding TCR recognition and the important limitations that remain.

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Benjie McMaster @benjamin-mcmaster.bsky.social · 20/07/2026

We then look at what drives the predictive ability of these models for TCR:pMHC predictions and investigate AF3's ability to understand T cell common-specificity and cross-reactivity.

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Benjie McMaster @benjamin-mcmaster.bsky.social · 20/07/2026

In our analysis, we set up a pipeline for running a large number of TCR:pMHC predictions and use it to benchmark the capabilities of AF2, AF3, Boltz-2, and Chai-1 at predicting T cell antigen specificity and TCR:pMHC complex structures.

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Benjie McMaster @benjamin-mcmaster.bsky.social · 20/07/2026

We speculated that these methods could provide a much-needed breakthrough to the field in generalising to new contexts in a perspective a couple of years ago (www.nature.com/articles/s41...). Last year, IMMREP25 (www.biorxiv.org/content/10.6...) validated this, showing the promise these models have.

nature.com

Can AlphaFold’s breakthrough in protein structure help decode the fundamental principles of adaptive cellular immunity? - Nature Methods

This Perspective discusses the potential of protein structure-prediction models for exploring the structural landscape and specificity of TCR–pMHC interactions.

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Benjie McMaster @benjamin-mcmaster.bsky.social · 20/07/2026

In this work, we set out to investigate the use of deep learning structure prediction to predict T cell antigen specificity.

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Reposted by Benjie McMaster

MRC Weatherall Institute of Molecular Medicine @imm.ox.ac.uk · 06/01/2026

#ScientistSpotlight This week we’re introducing Benjamin McMaster, a DPhil student at Hashem Koohy's Group here at the #MRCWIMM. @rdm.ox.ac.uk @medsci.ox.ac.uk @benjamin-mcmaster.bsky.social

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