The 48-Hour Cancer Binder
A multidisciplinary team participated in a 48-hour protein-design hackathon in Zurich, aiming to create a selective binder for the cancer-related protein FGFR2 while avoiding interaction with the similar FGFR1. Combining machine learning and biology expertise, they focused on designing a high-affinity, selective inhibitor using the iPSAE metric to evaluate binding confidence. The experience highlighted the importance of collaboration, efficient division of labor, and domain-specific knowledge in solving real-world biomedical problems.
- ▪The target protein was FGFR2, a receptor involved in cell growth that can promote cancer when overactive.
- ▪The team designed a binder to block FGFR2's interaction with FGF1 while ensuring it did not bind to the similar protein FGFR1 to avoid side effects.
- ▪Selectivity was measured using the iPSAE score, which quantified on-target binding to FGFR2 and minimized off-target binding to FGFR1.
- ▪The team split tasks by expertise, with biologists identifying target regions and ML specialists setting up generation and evaluation pipelines.
- ▪Structural similarity between FGFR2 and FGFR1 posed a major challenge, requiring precise design to achieve specificity.
Opening excerpt (first ~120 words) tap to expand
I am writing this blog post while on my way home from my first protein-design themed hackathon. Three days ago, when I first arrived in Zurich, I had no idea how it would turn out: as an ML person, I had general knowledge of protein design models but had never put it into practice on a real problem. Our team was a mix of CS and biology people, but none of us worked specifically in protein design.We still got to design the best binding protein on a real-world cancer problem.Besides sharing the technical details of the solution, I wanted to write this as a logbook on how to approach protein hackathons, and to make ML people less scared of this kind of domain.Problem and reasoningIn these hackathons, the structure is pretty clear: you are given a target protein and some constraints, and the…
Excerpt limited to ~120 words for fair-use compliance. The full article is at Ludocomito.
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