Biotechnology Data Provider: 24 Cataloged Datasets · Head-to-head
PubChem vs RCSB Protein Data Bank
Which biotechnology data provider: 24 cataloged datasets data fits your job: PubChem, or RCSB Protein Data Bank. API, files, or your warehouse. Daily, weekly, or hourly.
PubChem
RCSB Protein Data Bank
Where the fields line up
No shared field names. These two answer different questions.
| Field | PubChem | RCSB Protein Data Bank |
|---|---|---|
PUBCHEM_COMPOUND_CID | documented | not in this set |
PUBCHEM_MOLECULAR_FORMULA | documented | not in this set |
PUBCHEM_MOLECULAR_WEIGHT | documented | not in this set |
PUBCHEM_SMILES | documented | not in this set |
PUBCHEM_CONNECTIVITY_SMILES | documented | not in this set |
PUBCHEM_IUPAC_NAME | documented | not in this set |
PUBCHEM_IUPAC_INCHIKEY | documented | not in this set |
PUBCHEM_XLOGP3 | documented | not in this set |
PUBCHEM_CACTVS_TPSA | documented | not in this set |
PUBCHEM_HEAVY_ATOM_COUNT | documented | not in this set |
rcsb_id | not in this set | documented |
struct.title | not in this set | documented |
Coverage, side by side
| PubChem | RCSB Protein Data Bank | |
|---|---|---|
| Geographic | Global contributions from international depositors with no geographic restriction | Global depositions from structural biology laboratories worldwide; 82,833 entries cover human sequences |
| Temporal | Archive extends back to the 2004 launch | Continuous archive since 1971 - the longest-lived structured collection in the life sciences |
| Granularity | Per-compound, per-substance and per-bioassay records | Four levels: whole entry, polymer entity, biological assembly, individual atom coordinates |
What each contains
They tie on 1 attribute. Pick by fit, not by loyalty.
| PubChem | RCSB Protein Data Bank | |
|---|---|---|
| Steward | PubChem, a program of the U.S. National Center for Biotechnology Information | RCSB PDB, the US member of the worldwide Protein Data Bank consortium |
| Subject lens | Small-molecule chemistry: deposited substances, standardized unique compounds and the screening experiments run against them | Macromolecular structure: experimentally determined and computed 3D shapes of proteins, nucleic acids and their complexes with ligands |
| Record universe | Roughly 179.5 million compound identifiers carried in 359 compressed structure chunks of 85 to 535 MB each - tens of gigabytes compressed before annotations and 3D conformers | ~258,616 archived entries (~258,222 experimental, 394 integrative/hybrid) plus more than one million Computed Structure Models layered above (~992,732 from the AlphaFold DB, ~69,326 from ModelArchive) |
| Geographic coverage | Global contributions from international depositors with no geographic restriction | Global depositions from structural biology laboratories worldwide; 82,833 entries cover human sequences |
| Temporal reach | Archive extends back to the 2004 launch | Continuous archive since 1971 - the longest-lived structured collection in the life sciences |
| Finest granularity | Per-compound, per-substance and per-bioassay records | Four levels: whole entry, polymer entity, biological assembly, individual atom coordinates |
| Documented fields | 21 documented fields on the compound record, definitions verified | 19 documented fields on the entry record, definitions verified |
| Formats delivered | SDF, JSON, XML, CSV, TXT, PNG, ASN.1, RDF | mmCIF, legacy PDB, FASTA, SDF, JSON, XML |
| Rubric rating | 10 out of 10 (catalog average 7.81 across 1,744 datasets) | 10 out of 10 (catalog average 7.81 across 1,744 datasets) |
| Best for | Ligand chemistry: descriptors already computed, screening outcomes attached, scaffolds matched deterministically | Target structure: resolution-filtered coordinates, honest experimental-versus-computed tiers, citation-grade provenance |
Where they're equivalent
More than the molecule-versus-macromolecule split implies.
- Both sit at the top of the rubric: tied 10 out of 10, the highest mark in the Biotechnology slice, against a 7.81 catalog-wide average.
- Both dictionaries are fully verified, every definition checked rather than inferred - a standard met by 85.7 percent of the 1,744 cataloged datasets.
- Both draw on global depositor communities: international chemistry submissions on one side, worldwide structural biology laboratories on the other.
- Both share the identifier-name-mass-structure spine, and the spines interlock - RCSB ligand similarity runs on the SMILES and InChI notation PubChem issues.
- Both deliver overlapping formats: JSON and SDF appear in each record's format set, alongside XML on both sides.
- Both tie molecules to biology: PubChem through its Target tree of proteins, genes and pathways; RCSB through organism taxonomy tagged on every polymer entity.
- Neither substitutes for the other: no ligand descriptors or assay outcomes exist in the structure archive, and no coordinates exist in the compound repository.
Fair questions
Is PubChem better than the RCSB Protein Data Bank?
Different axes. PubChem holds roughly 179.5 million standardized small molecules with precomputed descriptors, linked bioassay outcomes and patent co-occurrence tables. The RCSB Protein Data Bank holds ~258,616 experimentally determined 3D structures of proteins and nucleic acids plus over a million computed models. Both score 10 out of 10 - the choice is ligand chemistry versus target structure, not quality.
Do the two field dictionaries overlap?
Only in the spine: a record identifier, a name or title, a mass and a structure representation. Beyond that they diverge - PubChem's twenty-one fields are computed physicochemical descriptors like XLogP3 and polar surface area, while RCSB's nineteen are experiment facts like determination method, resolution in angstroms and accession dates. The SMILES and InChI bridge connects the two chemistries.
Which archive reaches further back?
The RCSB Protein Data Bank, decisively. Its archive runs unbroken since 1971, making it the longest-lived structured collection in the life sciences - human deoxyhaemoglobin (4HHB) went in during 1984 and still resolves. PubChem reaches back to its 2004 launch. For forty-plus years of solved structures there is no comparable alternative.
Does one workflow ever need both?
Frequently - drug discovery is the textbook case. Virtual screening and QSAR run on PubChem's descriptor-complete compound rows; binding-site analysis and structural ML training run on RCSB's resolution-gated coordinates. The two interlock through SMILES and InChI ligand matching, so a ligand-versus-pocket study draws on both records at once.
Can I get both records from Datadory?
Yes - sample both, pick by fit, or take both in one feed. Each arrives normalized to its documented field dictionary with sample rows attached for validation, delivered on one schedule - daily, weekly, or hourly - your call - next to the rest of the biotechnology catalog.