BM_scaffold_ZINC

BM_scaffold_ZINC contains unique Bemis–Murcko (BM) scaffolds derived from the ZINC20 and ZINC22 drug-like molecules. These scaffolds are distributed as .smi text files for ease of streaming and tooling compatibility.

What’s included:

- data/standardized_BM_scaffolds_ZINC20.smi – BM scaffolds from ZINC20 drug-like molecules
- data/standardized_BM_scaffolds_ZINC22_parta.smi – BM scaffolds from ZINC22 drug-like molecules (part A)
- data/standardized_BM_scaffolds_ZINC22_partb.smi – BM scaffolds from ZINC22 drug-like molecules (part B)

Each file is one SMILES per line; no header.

Data provenance & scope

• Sources: ZINC20 and ZINC22 drug-like molecules (Downloaded 2024-10).
• Processing overview: BM scaffold extraction -> deduplication -> Standardization using MolVS -> save to .smi
• Notes: BM scaffolds from ZINC22 is partitioned into two .smi parts for practical file sizing on the Hub. The reason why we first extracted BM scaffold then standardization is also because the size of smi downloaded from ZINC22. Also, ZINC evolves; this snapshot may not reflect the latest available drug-like molecules especially from ZINC22.

Contact

Feel free to create an issue on github repo (https://github.com/Kartinaa/Benchmarking_gene_model) or email Bo Yang ([email protected]) or Dr. Jianing Li ([email protected]) if you have any questions!