Alternating Atomic and Token-Level Modeling Enabled AlphaFold 3 Small Molecules
Jeremy Wohlwend · 🔬Generating Molecules, Not Just Models · Feb 12, 2026 · at 29:20
Jeremy Wohlwend, co-founder of Boltz, explains architectural changes in AlphaFold 3 that enable multi-scale modeling across different molecular modalities.
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“The other part, I think that's enough for three is sort of this moving away from modeling just at the amino acid level to actually sort of having the model sort of alternate between you know, sort of atomic resolution modeling and then more like it's got token level, which is like at the amino acid level. That's also something that was introduced that I think, you know, was particularly helpful in like, you know, modeling these other modalities, like small molecule, et cetera.”
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