IQuestLab/UBio-Protein26

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).

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:

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

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

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

How to Load

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
• Code (E2Former-V2): https://github.com/IQuestLab/UBio-MolFM/tree/e2formerv2