---
tags:
  - protein structure prediction
  - MMseqs
  - Jackhmmer
language:
  - en
  - zh
license: other
---
<p align="center">
  <strong>
    <span style="font-size: 30px;">AlphaFold3 Dataset</span>
  </strong>
</p>

## Dataset Description

AlphaFold3_dataset is the companion dataset for the `OneScience-Group/AlphaFold3/` model. It includes inference input examples, public search databases, MMseqs databases, sharded Jackhmmer databases, and alignment-related directories. The dataset ID is fixed as `OneScience-Group/AlphaFold3_dataset`.

## Supported Tasks

This dataset supports the AlphaFold3 biomolecular structure prediction workflow. It provides both AlphaFold3 JSON examples that already contain MSAs and the database directories required to search for MSAs from sequences. The model can use these data for preflight checks, inference with MSAs, the MMseqs data pipeline, and the Jackhmmer data pipeline.

### Dataset Format and Structure

| Path | Type | Purpose | Required | Capability | Placement After Download | Notes |
|---|---|---|---|---|---|---|
| `manifest.yaml` | Manifest file | Machine-readable dataset description | Yes | All capabilities | Dataset package root directory | The LLM must parse this file |
| `onescience_run_manifest.yaml` | Runtime Manifest | Web interface read entry point | Yes | All capabilities | Dataset package root directory | Consistent with `manifest.yaml` |
| `metadata/file_manifest.yaml` | Integrity manifest | Records the source path, organized path, size, and SHA256 of key files | Yes | Preflight check | `metadata/` | Verifies consistency after organization |
| `scripts/validate_dataset.py` | Validation script | Checks directories, JSON schema, sizes, and SHA256 | Yes | Data read validation | `scripts/` | Does not run the model |
| `data/infer_input_data/` | Input examples | AlphaFold3 JSON examples containing all_data and pressure_data | Yes | Inference and preflight checks | `data/infer_input_data/` | The smallest example is `all_data/7r6r_data.json` |
| `data/public_databases/` | Public databases | Databases for Jackhmmer and template searches | Yes | Data pipeline | `data/public_databases/` | The upload view uses `pdb_2022_09_28_mmcif_files.tar` instead of the extracted `mmcif_files/` directory to avoid file-count limits |
| `data/mmseqsDB/` | MMseqs databases | MMseqs search databases | Yes | MMseqs data pipeline | `data/mmseqsDB/` | Includes small_bfd, mgnify, uniprot, and uniref90 |
| `data/jackhmmer_split/` | Sharded database | Sharded FASTA files for Jackhmmer searches | Yes | Jackhmmer data pipeline | `data/jackhmmer_split/` | See the directory filenames for the shard count |
| `data/alignDB/` | Alignment database | Alignment-related data | No | Advanced workflows | `data/alignDB/` | Optional |

## How to Use the Dataset
### Files and Download

Download the dataset:

```bash
hf download --dataset OneScience-Group/AlphaFold3_dataset
```

Download the compatible model:

```bash
hf download --model OneScience-Group/AlphaFold3/
```

If you use `--cache_dir`, you must switch to the root directory of the downloaded dataset package before validation.

### Data Placement

After downloading the dataset separately, you can run validation from the dataset package root directory. To use it with the model, place this repository's `data` subdirectory in the model package:

```text
<model-package>/data/alphafold3_dataset
```

You can do this by copying or linking the directory:

```bash
mkdir -p /path/to/model-package/data
ln -s /path/to/AlphaFold3_dataset/data /path/to/model-package/data/alphafold3_dataset
```

### Data Read Validation

Run the following command from the dataset package root directory:

```bash
python scripts/validate_dataset.py --root .
```

The validation script parses `metadata/file_manifest.yaml` and checks that key directories exist, JSON examples are readable, and filenames, sizes, and SHA256 values are consistent. On success, it outputs `dataset_validation_ok: true`.


## Official OneScience Information

| Platform | OneScience Main Repository | Skills Repository |
|---|---|---|
| Gitee |https://gitee.com/onescience-ai/onescience | https://gitee.com/onescience-ai/oneskills |
| GitHub | https://github.com/onescience-ai/OneScience | https://github.com/onescience-ai/oneskills |

## Limitations and License

mmseqs is a locally generated database. The public databases and AlphaFold3-related data are subject to their respective upstream licenses and terms of use.