README.md

---
pretty_name: CryoAtlas
license: cc-by-nc-4.0
tags:
- cryo-em
- structural-biology
- protein-structure
- benchmark
configs:
- config_name: catalog
  default: true
  data_files:
  - split: train
    path: resources/metadata/catalog/train.parquet
  - split: test
    path: resources/metadata/catalog/test.parquet
- config_name: benchmark_targets
  data_files:
  - split: test
    path: resources/metadata/catalog/benchmark_targets.parquet
- config_name: benchmark_results
  data_files:
  - split: test
    path: resources/benchmark/results.parquet
- config_name: examples
  data_files:
  - split: examples
    path: resources/benchmark/examples.parquet
- config_name: downloads
  data_files:
  - split: archives
    path: resources/metadata/catalog/archives.parquet
- config_name: training_utility
  data_files:
  - split: test
    path: resources/benchmark/training_utility/results.parquet
---

# CryoAtlas

A large curated dataset and unified benchmark for cryo-EM atomic model building.

*Accepted at NeurIPS 2026 · Evaluations & Datasets Track*

[Paper (OpenReview)](https://openreview.net/forum?id=qHJrv65ncA) · [Code](https://github.com/oulling/CryoAtlas-Code) · [Project website](https://oulling.github.io/cryoatlas/) · [3D Benchmark Explorer](https://oulling.github.io/cryoatlas/explore/)

CryoAtlas v1.0 provides **17,809 map–model–sequence entries** derived from EMDB and PDB records available up to March 2026: **16,657 training entries** and **1,152 test entries**, including the **618-target common benchmark**. The benchmark evaluates structural accuracy, map agreement and stereochemical quality.

## Download

| Folder | Contents | Compressed size |
|---|---|---:|
| [**train/**](https://huggingface.co/datasets/markfaa/CryoAtlas/tree/main/train) | Four disjoint training parts, 68 independent archives | 2.264 TB |
| [**test/**](https://huggingface.co/datasets/markfaa/CryoAtlas/tree/main/test) | Two archives: 618 benchmark targets + 534 remaining test entries | 150.9 GB |
| [**resources/**](https://huggingface.co/datasets/markfaa/CryoAtlas/tree/main/resources) | Benchmark resource package, metadata, indexes and download tools | Resource package: 1.90 GB |

**Start small:** [download the benchmark resource package](https://huggingface.co/datasets/markfaa/CryoAtlas/resolve/main/resources/CryoAtlas_v1.0_benchmark_resources.tar.gz) for baseline and retrained-ModelAngelo results, predicted structures and 10 complete examples. For selected training parts or an entry's containing archive, see the [download guide](resources/docs/downloads.md).

<a id="examples"></a>
## Explore online

- [**Entry catalog**](https://huggingface.co/datasets/markfaa/CryoAtlas/viewer/catalog/train): search EMD/PDB IDs, resolution and archive links.
- [**Benchmark results**](https://huggingface.co/datasets/markfaa/CryoAtlas/viewer/benchmark_results/test): 618 targets × five methods.
- [**Training utility**](https://huggingface.co/datasets/markfaa/CryoAtlas/viewer/training_utility/test): the two released ModelAngelo retraining conditions.
- [**Example previews**](https://huggingface.co/datasets/markfaa/CryoAtlas/viewer/examples/examples): density projections from 10 released examples.

The Viewer uses lightweight tables; maps, structures and sequences are in the archives. **The 618 benchmark targets are part of the 1,152-entry test set.**

![Dataset splits and resolution distributions](resources/docs/assets/dataset_overview.png)

## Documentation

[Croissant metadata](resources/metadata/croissant.json) · [Dataset guide](resources/docs/dataset_guide.md) · [Fields and metrics](resources/docs/data_dictionary.md) · [Archive checksums](resources/metadata/checksums/SHA256SUMS)

All 70 training/test archives have verified sizes and SHA-256 hashes. The download helper verifies selected archives automatically.

**License:** [CC BY-NC 4.0](https://creativecommons.org/licenses/by-nc/4.0/).