AlphaFold Resolves Protein Structures Using Dijkstra-Like Pairwise Distance Decoding
Gabriele Corso · 🔬Generating Molecules, Not Just Models · Feb 12, 2026 · at 20:48
Gabriele Corso, co-founder of Boltz, explains a mental model for how AlphaFold's architecture translates Multiple Sequence Alignments (MSA) into 3D structural predictions.
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“From this evolutionary information about potential contacts, Then it's almost as if the model is sort of running some kind of, you know, Diestro algorithm, where it's sort of decoding, okay, these have to be closed, okay, then if these are closed and this is connected to this, then this has to be somewhat closed, and so you decode, ah, this that becomes basically a pairwise kind of distance matrix, and then from this rough pairwise distance matrix, you decode kind of the actual potential structure.”
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