# Molecule datasets

Free, downloadable molecule datasets for docking and virtual screening, with structures, identifiers, and source links in CSV, JSON, and SDF.

Each set is compiled from public databases such as PubChem, ChEMBL, and ChEBI, and every row links back to its source record. Browse a table online, download it with license and citation details, or send the molecules straight into a docking, property, or screening tool.

[Search databases](https://proteiniq.io/app/databases)

## Research-ready datasets

Drug-like and biological molecule sets, plus docking benchmarks, for virtual screening, redocking, and property work.

[2,104 molecules Approved drugs 2,104 approved small-molecule drugs from ChEMBL with SMILES, PubChem CIDs, drug-likeness descriptors, mechanisms, ATC classes, and an FDA status checked against Drugs@FDA. Download as CSV, JSON, or a docking-ready 3D SDF. CSV, JSON, SDF · CC BY-SA 3.0 · Updated October 5, 2026](https://proteiniq.io/datasets/small-molecule-drugs)[184 molecules Biological molecules A curated list of small biological molecules, metabolites, cofactors, amino acids, nucleobases, lipids, and related structures. CSV, JSON · CC BY 4.0 · Updated October 5, 2026](https://proteiniq.io/datasets/biological-molecules)[428 complexes PoseBusters Benchmark set Index of the 428 recent protein-ligand crystal structures in the PoseBusters docking benchmark, with the 308-complex subset flagged, ligand SMILES, and RCSB links. CSV, JSON · CC BY 4.0 · Updated October 5, 2026](https://proteiniq.io/datasets/posebusters-benchmark)[85 complexes Astex Diverse Set Index of the 85 protein-ligand complexes in the Astex Diverse Set, the classic redocking benchmark, with ligand SMILES, resolution, and RCSB links. CSV, JSON · CC BY 4.0 · Updated October 5, 2026](https://proteiniq.io/datasets/astex-diverse-set)

## Chemistry reference lists

General chemistry lists for teaching, quick lookups, and worked examples.

[163 molecules Organic compounds A practical list of common and important organic compounds grouped by functional class, with structures and source identifiers. CSV, JSON · CC BY-SA 3.0 · Updated October 5, 2026](https://proteiniq.io/datasets/organic-compounds)[101 molecules Common molecules Everyday molecules and compounds from air, food, household products, fuels, and industry, each with a category that explains where you meet it. CSV, JSON · CC BY 4.0 · Updated October 5, 2026](https://proteiniq.io/datasets/common-molecules)[136 molecules Polar and nonpolar molecules Polar and nonpolar molecules with a specific reason for each classification, the molecular geometry, and experimental dipole moments where available. CSV, JSON · CC BY 4.0 · Updated October 5, 2026](https://proteiniq.io/datasets/polar-and-nonpolar-molecules)[160 molecules Alkane isomers Every constitutional isomer of the alkanes from methane (CH4) to decane (C10H22), 150 structures in total, plus the straight-chain alkanes up to C20. CSV, JSON · CC BY 4.0 · Updated October 5, 2026](https://proteiniq.io/datasets/alkane-isomers)[43 molecules Diatomic and monatomic elements A reference list of true diatomic molecules (the seven elemental diatomics, heteronuclear and interhalogen molecules, and reactive gas-phase species) and the monatomic noble gases, with formulas and PubChem identifiers. CSV, JSON · CC BY 4.0 · Updated October 5, 2026](https://proteiniq.io/datasets/diatomic-and-monatomic-elements)