| --- |
| 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.** |
|
|
|  |
|
|
| ## 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/). |
|
|
