Caizus/natural-product-protein-interact

NPPI-Net reproducibility resources

This dataset repository contains the exact large inputs used by the retained NPPI-Net S1-S4 result chain. Source code, fixed split manifests, paper configurations, raw metrics, and verification scripts are published separately in Cai-z-us/natural-product-protein-interact. Paper tables and images are not duplicated here.

Files

Path	Purpose	Bytes	SHA256
data/dataset_all.csv	canonical headerless interaction dataset	23,281,585	0bef27914ed06e5fe0af9ad64ecd16f27d007369b738f65240795505708d8017
data/external/uniprot_human_reviewed.fasta	exact historical reviewed-human UniProtKB snapshot	13,663,585	89b398077ec571c34bd67fd10fc1640eeae37d1421d6f84c3a8a94e1db88dac3
data/mol/unimol_v2_1.1B.pth	pooled Uni-Mol2 molecule representations	1,460,616,917	f87c3673e911e1cc21022e4c4ddcb40cfb2b9ee4e355899ba02f60ae21ad83da
data/prot/proteinglm_xtmlm_1b.pth	pooled ProteinGLM protein representations	9,691,794,119	1abb24b598db851733b7345618284aab78ef0ce4d431b454878fa63451d20cb4

The CSV has 32,802 rows, 8,959 unique molecule identifiers, 1,860 unique protein identifiers, and no header. Its ten columns are, in order: mol_id, smiles, uniprot_id, sequence, pchembl, standard_relation, standard_value_nM, standard_units, standard_type, and confidence_score.

The retained model consumes pooled float32 vectors only: 1,536 dimensions for molecules and 2,048 for proteins. Token inputs are disabled in the paper configuration.

Download and verify

From the root of a clone of the source repository:

hf download Caizus/natural-product-protein-interact \
  --repo-type dataset \
  --revision d67ea7b4f75b35f1f362caebcd3d5565cedc16dc \
  --local-dir .
sha256sum --check SHA256SUMS
uv run --frozen python scripts/verify_resources.py --deep

scripts/verify_resources.py checks byte size, SHA256, schema, key alignment, pooled dimensions, and dtypes against artifacts/resources/manifest.yaml. PyTorch files are opened with the restricted weights_only loader.

Provenance

• The canonical interaction dataset was built from ChEMBL 34 and a reviewed human UniProtKB snapshot. The exact FASTA is published above because the historical UniProt release response header was not retained; its byte identity, rather than an inferred release number, is authoritative.
• The molecule file was generated with unimol-tools==0.1.5 and Uni-Mol2 1.1B. The package wheel and final output are content-addressed in the source repository.
• The protein file was generated from biomap-research/proteinglm-1b-mlm at revision 676c1bcb9f737c166a25587f83fd580610acb1ad.

See ARTIFACTS.md, DATASET.md, and THIRD_PARTY_NOTICES.md for the full build and attribution record.

Terms

This repository contains artifacts with different governing terms; the project's future source-code license does not replace them.

• ChEMBL-derived dataset content is subject to ChEMBL 34's CC BY-SA 3.0 terms and required attribution.
• UniProt-derived content is subject to CC BY 4.0 attribution.
• Uni-Mol tooling/model attribution is retained; applicable source-data terms continue to apply to the generated molecule representations.
• ProteinGLM is CC BY-NC 4.0. The generated protein representations must be treated as noncommercial material and must not be advertised as unrestricted commercial assets.

No additional artifact-wide license is asserted beyond those file-specific terms while the authors finalize the paper release metadata.