> ## Documentation Index
> Fetch the complete documentation index at: https://docs.biohub.ai/llms.txt
> Use this file to discover all available pages before exploring further.

# ESMC

> Embed sequences, score mutations, interpret SAE features, and fine-tune ESMC.

<Card title="View tutorials on GitHub" icon="github" href="https://github.com/Biohub/esm/tree/main/cookbook/tutorials" horizontal />

<Columns cols={2}>
  <Card title="Embedding sequences with ESMC" icon="https://mintlify.s3.us-west-1.amazonaws.com/biohub-8940d923/icons/colab.svg" href="https://colab.research.google.com/github/Biohub/esm/blob/main/cookbook/tutorials/embed.ipynb">
    Embed protein sequences and explore how different transformer layers encode structural and
    functional information.
  </Card>

  <Card title="Zero-shot entropy and mutation analysis" icon="https://mintlify.s3.us-west-1.amazonaws.com/biohub-8940d923/icons/colab.svg" href="https://colab.research.google.com/github/Biohub/esm/blob/main/cookbook/tutorials/esmc_mutation_scoring.ipynb">
    Compute per-position entropy and log-likelihood ratios to identify constrained vs.
    mutation-tolerant sites.
  </Card>

  <Card title="Layer sweep for enzyme function classification" icon="https://mintlify.s3.us-west-1.amazonaws.com/biohub-8940d923/icons/colab.svg" href="https://colab.research.google.com/github/Biohub/esm/blob/main/cookbook/tutorials/esmc_layer_sweep.ipynb">
    Learn how to sweep all layers to find which one is best using enzyme classification as a task.
  </Card>

  <Card title="Understanding proteins with SAE features" icon="https://mintlify.s3.us-west-1.amazonaws.com/biohub-8940d923/icons/colab.svg" href="https://colab.research.google.com/github/Biohub/esm/blob/main/cookbook/tutorials/esmc_sae_feature_interpretation.ipynb">
    Extract and visualize sparse autoencoder features, rank by peak activation, and map activations
    onto 3D structures.
  </Card>

  <Card title="Fine-tuning ESMC" icon="https://mintlify.s3.us-west-1.amazonaws.com/biohub-8940d923/icons/colab.svg" href="https://colab.research.google.com/github/Biohub/esm/blob/main/cookbook/tutorials/esmc_finetune.ipynb">
    Fine-tune a classification or regression head for your dataset on top of ESMC using Parameter
    Efficient Fine-tuning (PEFT).
  </Card>
</Columns>