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The Illustrated AlphaFold

A visual walkthrough of the AlphaFold3 architecture, with more details and diagrams than you were probably looking for.

We also include a linear embedding of the inverse square of the distances, add to it a projection of c l and c m, and update this with a few more linear layers with residual connectionsThe AF3 paper doesn't really clarify why this additional inverse distance step is performed or contain ablations for their effect of it; so, as with many of the steps we will discuss, we can only assume they were empirically shown to be useful.In the AF3 supplement, the p tensor is typically referred to in its vector form p l,m(where this represents the relationship between atom l and atom m).. In this section we spend significant time on two operations: The Outer Product Mean enables m to influence z updates m based on z and is a simplified version of attention with pair-bias (intended for MSAs) This type of data augmentation was popularize with CNNs but in the past few years, equivariant architectures like IPA have been considered an more efficient and elegant approach to solve the same problem.

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