---
license: mit
tags:
- chemistry
- biology
---
**(At present, only download applications from universities or certified non-profit organizations are accepted.)**

This repository provides the **UBio-Protein26 5M** dataset release used in the UBio-MolFM project:
**"UBio-MolFM: A Universal Molecular Foundation Model for Bio-Systems"** ([link](https://arxiv.org/abs/2602.17709)).

UBio-Protein26 5M is a protein-focused subset of UBio-Mol26, including solvated tripeptides and residue-centered protein clusters.

## Computational Details

All labels are generated from DFT calculations for physically consistent force-field training.

- Functional: **ωB97M-D3** , following the setup described in the report.
- Basis sets:
  - **def2-SVP** subset (majority, efficient large-scale coverage)
  - **def2-TZVPD** subset (high-fidelity subset; in practice with mixed-basis treatment for H/metal atoms as described in the report)
- System scale: up to approximately **1,200 atoms**.
- Training set size: **5M** samples
  - def2-SVP: **4500K**
  - def2-TZVPD: **500K**
- Test set size: **200K** samples
  - def2-SVP: **180K**
  - def2-TZVPD: **20K**
- Total size: **5.2M** samples.

Note: The release name "5M" refers to the rounded training scale (about 5.0M) plus a 0.2M test split.

## Dataset Layout
The data is split first by `train/test`, then by basis set:

```text
UBio-Protein26-5M/
├── train/
│   ├── def2-svp/
│   └── def2-tzvpd/
└── test/
    ├── def2-svp/
    └── def2-tzvpd/
```

All shards are in LMDB format (`data_XXXXX.lmdb`).

![image](https://cdn-uploads.huggingface.co/production/uploads/6954878be1200d74c1c7abc9/d0njajyr-gX8Nk7YM25Ah.png)

*Figure: Structural distribution of UBio-Protein26 5M, consistent with the report resources section.*

## How to Load

```python
import lmdb
import pickle

lmdb_path = "train/def2-svp/data_00001.lmdb"

env = lmdb.open(lmdb_path, readonly=True, lock=False, subdir=False)
samples = []

with env.begin() as txn:
    # Dataset length is stored explicitly in LMDB.
    n = int(txn.get("length".encode()))
    for i in range(n):
        raw = txn.get(f"{i}".encode())
        if raw is not None:
            samples.append(pickle.loads(raw))

env.close()

if samples:
    print(samples[0].keys())
```

To compute total sample size for a split, sum `length` across all LMDB shards in that split/basis directory.

## Data Fields

This processed release keeps only the following fields:

- `charge`
- `multiplicity`
- `pos` (shape `[N, 3]`, Angstrom)
- `atomic_numbers` (shape `[N]`)
- `energy` (unit: `kcal/mol`)
- `forces` (shape `[N, 3]`, unit: `kcal/mol/Å`)

Other auxiliary fields from upstream pipelines are intentionally removed.

## Reference

- Paper: [**UBio-MolFM: A Universal Molecular Foundation Model for Bio-Systems**](https://arxiv.org/abs/2602.17709)
- Code: https://github.com/IQuestLab/UBio-MolFM