BioTech Encyclopedia

Protein language models (ESM): uses in research

Also: ESM, ESMFold

AI models trained on millions of protein sequences, the way chatbots are trained on text.

Known properties: Protein language models (ESM)

Only what the cited papers report.

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Timeline

  1. 2021 Learning biology from 250 million sequences
  2. 2023 ESMFold and the Metagenomic Atlas

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lab computing 2021

Learning biology from 250 million sequences

Rives and colleagues trained a language model on 86 billion amino acids from 250 million proteins; its learned representations encoded structure and enabled state-of-the-art prediction of mutation effects.

As reported in: Rives, Meier, Sercu et al. (2021). Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences. Proceedings of the National Academy of Sciences. doi:10.1073/pnas.2016239118

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commercial computing 2023

ESMFold and the Metagenomic Atlas

Lin and colleagues scaled protein language models to 15 billion parameters, predicting atomic-level structure up to 60× faster, and predicted over 617 million metagenomic protein structures.

As reported in: Lin, Akin, Rao et al. (2023). Evolutionary-scale prediction of atomic-level protein structure with a language model. Science. doi:10.1126/science.ade2574

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