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imathur1 merged 1 commit into from
Jul 24, 2026
Merged

sae notebook sync #368

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2 changes: 1 addition & 1 deletion README.md
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# A world model of protein biology: ESMC, ESMFold2, & ESM Atlas


[ESMC & ESMFold2 Preprint](https://www.biorxiv.org/content/10.64898/2026.06.03.729735) &sdot; [Atlas](https://biohub.ai/esm/protein/atlas) &sdot; [Tutorials](https://github.com/Biohub/esm/tree/main/cookbook/tutorials) &sdot; [Slack](https://join.slack.com/t/biohub-community/shared_invite/zt-3yxdy77dv-rJHI97SprbDXwEYP3Y1tqQ)<br>
[ESMC & ESMFold2 Preprint](https://www.biorxiv.org/content/10.64898/2026.06.03.729735) &sdot; [Atlas](https://biohub.ai/esm/protein/atlas) &sdot; [Tutorials](https://github.com/Biohub/esm/tree/main/cookbook/tutorials) &sdot; [Slack](https://bit.ly/esm-slack)<br>
</div>

We are releasing a world model for protein biology: a scientific engine for prediction, design, and discovery. Built on the latest generation of Evolutionary Scale Modeling (ESM), this system learns from the protein sequences produced by evolution and uses that knowledge to represent, map, predict, and design proteins across scales — from atomic interactions to evolutionary relationships spanning billions of years. The system includes three artifacts: ESMC, ESMFold2, and ESM Atlas.
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7 changes: 4 additions & 3 deletions cookbook/tutorials/binder_design.ipynb
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"outputs": [],
"source": [
"# ---- Monitor ----\n",
"# Tail a function's output here in jupyter\n",
"# Tail a function's output here in jupyter. Interrupt the kernel to stop the tail.\n",
"! modal app logs esmfold2-design -f --function-call {future.object_id}"
]
},
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" target=targets,\n",
" binder=binders,\n",
" use_scaling_critics=[True],\n",
" seed=list(range(128)),\n",
" batch_size=[1],\n",
" seed=list(range(16)),\n",
" # NOTE - reduce if you want lower latency to get results.\n",
" batch_size=[6],\n",
")\n",
"df = pd.DataFrame(product(*line_sweeps.values()), columns=line_sweeps.keys())\n",
"df[\"target_name\"], df[\"target_sequence\"] = zip(*df[\"target\"], strict=True)\n",
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