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AI Advances in Protein Folding and Variant Effect Prediction

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The 2024 Nobel Prize in Chemistry was awarded for computational protein design and AI-driven protein structure prediction breakthroughs, highlighting the impact of Rosetta and AlphaFold. What are the architectural differences between AlphaFold2 and AlphaFold3? How might the emergence of AlphaGenome shape the future landscape of in-silico variant effect prediction tools?

The journal club will discuss:

Predicting Splicing from Primary Sequence with Deep Learning (Illumina, 2019) https://www.cell.com/cell/fulltext/S0092-8674(18)31629-5

Highly accurate protein structure prediction with AlphaFold (DeepMind, 2021) https://www.nature.com/articles/s41586-021-03819-2

Effective gene expression prediction from sequence by integrating long-range interactions (DeepMind, 2021) https://www.nature.com/articles/s41592-021-01252-x

Accurate structure prediction of biomolecular interactions with AlphaFold 3 (DeepMind, 2024) https://www.nature.com/articles/s41586-024-07487-w

Advancing regulatory variant effect prediction with AlphaGenome (DeepMind, 2026) https://www.nature.com/articles/s41586-025-10014-0

This talk is part of the DAMTP ML for Science Reading Group series.

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