Covariation made AlphaFold and LLMs possible — small molecules need equivalent data

proteinrosh · x · 2026-11-04

sokrypton and proteinrosh debate how small-molecule AI could replicate AlphaFold's success:

sokrypton: protein breakthroughs came from covariation data enabled by genomics/metagenomics; for small molecules we need ways to identify ligand presence/absence across the whole tree of life.
proteinrosh: sequencing is cheap and informative on its own — coevolution data just happened to become cheap to collect via sequencing.
sokrypton: covariation is the key ingredient (for LLMs too), so other modalities need equivalent data collected under natural or artificial selection — before biodiversity goes extinct.

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