> ## 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.

# ESM Atlas API

> Summary of the ESM Atlas REST endpoints for proteins, clusters, SAE features, similarity search, and batch lookup.

The [ESM Atlas](https://docs.biohub.ai/learn/guides/esm-atlas) is an open-access resource of predicted protein structures and interpretable feature annotations.
The ESM Atlas API exposes the same data through REST endpoints at `https://biohub.ai/esm/protein/api/v1alpha1`.
Atlas REST endpoints are public and do not require an API key.
The API version is `v1alpha1`, so interfaces may change without notice.

Most endpoints identify a protein by its `protein_hash`, the MD5 hash that the Atlas uses as the protein's ID.
If you start from a UniProtKB accession, call [Resolve UniProt ID](https://docs.biohub.ai/api/protein/atlas/proteins/uniprot.md) first to get the `protein_hash`.

## Proteins

| Endpoint | Purpose |
| - | - |
| [Get Protein](https://docs.biohub.ai/api/protein/atlas/proteins/get.md) | Return a protein's metadata, amino-acid sequence, and top-activating SAE features. |
| [Get Thumbnail](https://docs.biohub.ai/api/protein/atlas/proteins/thumbnail.md) | Return a pre-rendered PNG thumbnail of a protein's predicted structure. |
| [Resolve UniProt ID](https://docs.biohub.ai/api/protein/atlas/proteins/uniprot.md) | Resolve a UniProtKB accession or entry name to its protein record and `protein_hash`. |

## Batch lookup

Batch lookup retrieves data for many proteins in one request.
Small batches return a zip file directly with status `200`.
Large batches return a job handle with status `202`, which you poll until the zip file is ready.

| Endpoint | Purpose |
| - | - |
| [Batch Lookup](https://docs.biohub.ai/api/protein/atlas/proteins/batch.md) | Look up multiple proteins by `protein_hash`. |
| [Poll Batch Job](https://docs.biohub.ai/api/protein/atlas/proteins/batch-status.md) | Check an async batch job and get its zip download URL when it completes. |
| [Cancel Batch Job](https://docs.biohub.ai/api/protein/atlas/proteins/batch-cancel.md) | Request cancellation of an async batch job. |

## Clusters and similarity

| Endpoint | Purpose |
| - | - |
| [Get Cluster](https://docs.biohub.ai/api/protein/atlas/clusters.md) | Return cluster metadata and member protein hashes for a cluster representative protein. |
| [Similarity Search](https://docs.biohub.ai/api/protein/atlas/similarity-search.md) | Submit an amino-acid sequence and find Atlas proteins with similar SAE feature vectors. |

## SAE features

Sparse autoencoder (SAE) features are interpretable signals learned from the ESMC protein language model.

| Endpoint | Purpose |
| - | - |
| [List SAE Features](https://docs.biohub.ai/api/protein/atlas/features/list.md) | Return every SAE feature with its index, label, and description. |
| [Get SAE Feature](https://docs.biohub.ai/api/protein/atlas/features/detail.md) | Return full metadata for one feature, including top activating proteins and activation statistics. |

## Next steps

For step-by-step examples that combine these endpoints, see the [Atlas API guides](https://docs.biohub.ai/learn/tutorials/atlas/overview).
To query the Atlas from an AI assistant without writing code, use [Biohub MCP](https://docs.biohub.ai/biohub-mcp/overview.md).


## Related topics

- [Atlas API guides](https://docs.biohub.ai/learn/tutorials/atlas/overview.md)
- [ESM Atlas](https://docs.biohub.ai/learn/guides/esm-atlas.md)
- [ESMC](https://docs.biohub.ai/models/esmc.md)
- [ESMFold2](https://docs.biohub.ai/models/esmfold2.md)
- [Biohub MCP ESM Atlas tools reference](https://docs.biohub.ai/biohub-mcp/esm-atlas-tools.md)