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The “AlphaFold moment” for protein binder design might be imminent
Accelerated by protein design competitions
In a letter earlier this year on Nature Biotechnology, Roberto Chica and Noelia Ferruz wondered “What does it take for an ‘AlphaFold Moment’ in functional protein engineering and design?”.[1] Their main point, which I fully agree with, is that the central challenge in functional protein design is much harder to define as a closed-form question — and hence to evaluate — than CASP’s clearer question of “How does this protein fold in 3D?”
Defining what makes a designed protein a “good design” is much more complex, as it can involve multiple factors such as binding affinity, stability, enzymatic activity, etc. depending on the problem meant to be tackled by the design. This diversity complicates the creation of standardized performance metrics, making a CASP-like assessment for protein design far more elusive.
However, despite these significant challenges, recent scientific advances including but not limited to the 2024 Nobel Prize in Chemistry,[2] highlight how quickly the field of protein (modeling and) design is evolving. In this context, I’m here to discuss the outcomes of recent protein design competitions, especially those by companies flourishing now with semi-automated labs for mid- to high-throughput…