license: mit
tags:
- chemistry
- biology
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:
chargemultiplicitypos(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.