# io.github.cyanheads/pubchem-mcp-server

> Search PubChem compounds, properties, safety data, bioactivity, and cross-references.

- name: io.github.cyanheads/pubchem-mcp-server
- version: 0.7.0
- connection class: R0 (autonomous)
- trust: 94/100
- quality: 73/100 (needs work)
- owner: not claimed
- descriptor: https://api.protogrid.dev/v1/servers/io.github.cyanheads%2Fpubchem-mcp-server
- tools: https://api.protogrid.dev/v1/servers/io.github.cyanheads%2Fpubchem-mcp-server/tools

**An agent can connect right now, no human step.** Remote endpoint, no authentication, reachable on the last probe.

## Connection (mcpServers)

```json
{
  "mcpServers": {
    "pubchem-mcp-server": {
      "type": "http",
      "url": "https://pubchem.caseyjhand.com/mcp"
    }
  }
}
```


## Trust

- hygiene: 100
- liveness: 100
- freshness: 100
- provenance: 80
- drivers: +repository +namespace-matches-repo +reachable +uptime-100% +updated-6d-ago
- Derived from observable signals (official registry feed and our own credential-free probes); no code audit performed.

## Quality 73/100 (needs work)

### protocol: 88 (weight 25)

- pass `protocol.modern`: supports 2026-07-28 (server/discover)
- pass `protocol.stateless`: answers without a session
- pass `protocol.transport`: streamable HTTP
- warn `protocol.list_ttl`: tools/list declares ttlMs 0, so clients re-fetch it on every use

### authorization: n/a (weight 15)

- n/a `auth.prm`, `auth.as_metadata`, `auth.cimd`: no remote uses OAuth
- n/a `auth.secret_in_url`: no templated URL

### tool hygiene: 86 (weight 30)

- pass `tools.descriptions`: every tool has a description
- pass `tools.description_length`: descriptions are concise
- pass `tools.schemas`: every tool has an object input schema
- pass `tools.annotations`: 10 of 10 tools declare readOnlyHint or destructiveHint
- fail `tools.directory_hints`: no tool declares all four of readOnlyHint, destructiveHint, idempotentHint and openWorldHint; missing: pubchem_get_compound_image (destructiveHint); pubchem_get_compound_3d_structure (destructiveHint); pubchem_get_compound_xrefs (destructiveHint); …
- pass `tools.token_cost`: about 5,862 tokens to load every tool
- pass `tools.api_dump`: tools are not a one-to-one API dump

### stability: 25 (weight 15)

- warn `stability.changes`: 20 tool changes in 30 days
- fail `stability.rug_pull`: 1 tools kept their name but changed most of their description in 30 days; review before trusting them

### dependencies: n/a (weight 15)

- n/a `deps.known_vulns`, `deps.mcp_sdk_version`, `deps.resolvable`: deps.dev does not know @cyanheads/pubchem-mcp-server@0.7.0, @cyanheads/pubchem-mcp-server@0.7.0

- tools: 10, about 5,862 tokens to load them all
- tool set hash: 3a1a8dc1d5b87b53adf5d6b317dc89a0
- tools last changed: 2026-10-15T07:12:31.298Z
- badge: [![protogrid quality](https://protogrid.dev/badge/io.github.cyanheads/pubchem-mcp-server.svg)](https://protogrid.dev/servers/io.github.cyanheads/pubchem-mcp-server)
- Checks run on what our credential-free, read-only probes observe; tools are never called and no code audit is performed.

### Tool changes

- 2026-10-15 `pubchem_get_summary` changed (description, inputSchema, outputSchema)
  - before: Get descriptive summaries for PubChem entities by ID. Supports assays (AID), genes (Gene ID), proteins (UniProt accession), and taxonomy (Tax ID). Up to 10 per call.
  - after: Get descriptive summaries for PubChem entities by ID. Supports assays (AID), genes (Gene ID), proteins (UniProt accession), and taxonomy (Tax ID). Up to 10 per call; identifiers past that are returned in unprocessed for a follow-up call.
- 2026-10-15 `pubchem_search_assays` changed (inputSchema, outputSchema)
- 2026-10-15 `pubchem_get_compound_interactions` changed (description, inputSchema, outputSchema)
  - before: Get a compound's interaction data: drug-drug interactions (DrugBank), drug-food interactions, and chemical-target interactions (binding/activity from BindingDB, ChEMBL, and others). Each entry carries its originating source. Results are paged per kind, with the source-record total and the next offset reported for each. Richest for approved drugs; many compounds have no deposited interaction records.
  - after: Get a compound's interaction data: drug-drug interactions (DrugBank), drug-food interactions, and chemical-target interactions (binding/activity from BindingDB, ChEMBL, and others). Each entry carries its originating source. Results are paged per kind, with the source-record total and the next offset reported for each. Richest for approved drugs; many compounds have no deposited interaction records. Drug-drug and target interactions come from PubChem's SDQ service, which can refuse automated requests — a refused kind is reported in failedKinds while the others still return; per-target activity is also available from pubchem_get_bioactivity.
- 2026-10-15 `pubchem_get_bioactivity` changed (inputSchema, outputSchema)
- 2026-10-15 `pubchem_get_compound_safety` changed (description, inputSchema, outputSchema) **meaning changed**
  - before: Get GHS (Globally Harmonized System) hazard classification and safety data for one or more compounds by CID. Returns signal word, pictograms, hazard statements (H-codes), and precautionary statements (P-codes) per compound. Data sourced from PubChem depositors — source attribution included.
  - after: Get GHS (Globally Harmonized System) hazard classification and safety data for one or more compounds by CID. Returns signal word, pictograms, hazard statements (H-codes), and precautionary statements (P-codes) per compound, merged across sources, plus each source's own classification — its signal word, pictograms, H-codes with ECHA notifier agreement percentages, and notification counts — since sources often disagree. Reports ECHA "Not Classified" verdicts as their own status.
- 2026-10-15 `pubchem_get_compound_xrefs` changed (description, inputSchema, outputSchema)
  - before: Get external database cross-references for a compound: PubMed citations, patent IDs, gene/protein associations, registry numbers, and taxonomy IDs. Results are paged per type — capped at maxPerType with the total count reported; reach the IDs past a page with offset.
  - after: Get external database cross-references for a compound: PubMed citations, patent IDs, gene/protein associations, registry numbers, and taxonomy IDs. Results are paged per type — capped at maxPerType with the total count reported; reach the IDs past a page with offset. PubMed IDs come highest (most recently assigned) first and the other numeric types in ascending order; string IDs keep PubChem's order.
- 2026-10-15 `pubchem_get_compound_3d_structure` changed (inputSchema)
- 2026-10-15 `pubchem_get_compound_image` changed (inputSchema)
- 2026-10-15 `pubchem_get_compound_details` changed (description, inputSchema, outputSchema)
  - before: Get detailed compound information by CID. Returns physicochemical properties (molecular weight, SMILES, InChIKey, XLogP, TPSA, etc.), optionally with a textual description (pharmacology, mechanism, therapeutic use), known synonyms, drug-likeness assessment (Lipinski/Veber rules), and/or pharmacological classification (FDA classes, MeSH classes, ATC codes). Accepts up to 100 CIDs per call.
  - after: Get detailed compound information by CID. Returns physicochemical properties (molecular weight, SMILES, InChIKey, XLogP, TPSA, etc.), optionally with a textual description (pharmacology, mechanism, therapeutic use), known synonyms, drug-likeness assessment (Lipinski/Veber rules), and/or pharmacological classification (FDA classes, MeSH classes, ATC codes). Fetches up to 100 CIDs per call; CIDs past that are returned in unprocessed for a follow-up call.
- 2026-10-15 `pubchem_search_compounds` changed (description, inputSchema, outputSchema)
  - before: Search PubChem for chemical compounds by identifier (name, SMILES, or InChIKey, batched up to 25), molecular formula in Hill notation, substructure or superstructure containment, or 2D Tanimoto similarity. Returns a page of CIDs — reach matches past maxResults with offset. Optionally hydrate results with properties to avoid a follow-up pubchem_get_compound_details call.
  - after: Search PubChem for chemical compounds by identifier (name, SMILES, or InChIKey, up to 25 per call), molecular formula in Hill notation, substructure or superstructure containment, 2D Tanimoto similarity, or the compounds a bioassay (AID) found active or tested. Returns a page of CIDs — reach matches past maxResults with offset. Optionally hydrate results with properties to avoid a follow-up pubchem_get_compound_details call.

Full history: https://api.protogrid.dev/v1/servers/io.github.cyanheads%2Fpubchem-mcp-server/changes

## Dependencies

- npm @cyanheads/pubchem-mcp-server@0.7.0: unknown
- npm @cyanheads/pubchem-mcp-server@0.7.0: unknown

Dependency graphs from deps.dev; advisories from OSV.dev, including the GitHub Advisory Database and the PyPI Advisory Database; all CC BY 4.0.

## Remotes

- https://pubchem.caseyjhand.com/mcp (streamable-http, auth none, reachable true, uptime30d 1)

## Packages

- npm @cyanheads/pubchem-mcp-server@0.7.0
- npm @cyanheads/pubchem-mcp-server@0.7.0

## Tools (10)

- `pubchem_get_bioactivity`: Get a compound's bioactivity profile: which assays tested it, activity outcomes (Active/Inactive/Inconclusive), target identifiers (NCBI Gene ID, UniProt/GenBank accession), and quantitative values (IC50, EC50, Ki, etc.). Filter by outcome and/or a specific molecular target (NCBI Gene ID or protein accession) to focus the profile — e.g. "is this compound active against target T?".
- `pubchem_get_compound_3d_structure`: Get a compound's default 3D conformer — atomic coordinates and bonds — for one CID. format="json" (default) returns atoms and bonds parsed into structured fields; format="sdf" returns the raw V2000 SDF text for passthrough to docking, rendering, or conformer tools. Optionally lists alternate conformer IDs. Not every compound has computed 3D coordinates (large molecules, mixtures, and some salts do not).
- `pubchem_get_compound_details`: Get detailed compound information by CID. Returns physicochemical properties (molecular weight, SMILES, InChIKey, XLogP, TPSA, etc.), optionally with a textual description (pharmacology, mechanism, therapeutic use), known synonyms, drug-likeness assessment (Lipinski/Veber rules), and/or pharmacological classification (FDA classes, MeSH classes, ATC codes). Fetches up to 100 CIDs per call; CIDs past that are returned in unprocessed for a follow-up call.
- `pubchem_get_compound_image`: Fetch a 2D structure diagram (PNG image) for a compound by CID.
- `pubchem_get_compound_interactions`: Get a compound's interaction data: drug-drug interactions (DrugBank), drug-food interactions, and chemical-target interactions (binding/activity from BindingDB, ChEMBL, and others). Each entry carries its originating source. Results are paged per kind, with the source-record total and the next offset reported for each. Richest for approved drugs; many compounds have no deposited interaction records. Drug-drug and target interactions come from PubChem's SDQ service, which can refuse automated requests — a refused kind is reported in failedKinds while the others still return; per-target activity is also available from pubchem_get_bioactivity.
- `pubchem_get_compound_safety`: Get GHS (Globally Harmonized System) hazard classification and safety data for one or more compounds by CID. Returns signal word, pictograms, hazard statements (H-codes), and precautionary statements (P-codes) per compound, merged across sources, plus each source's own classification — its signal word, pictograms, H-codes with ECHA notifier agreement percentages, and notification counts — since sources often disagree. Reports ECHA "Not Classified" verdicts as their own status.
- `pubchem_get_compound_xrefs`: Get external database cross-references for a compound: PubMed citations, patent IDs, gene/protein associations, registry numbers, and taxonomy IDs. Results are paged per type — capped at maxPerType with the total count reported; reach the IDs past a page with offset. PubMed IDs come highest (most recently assigned) first and the other numeric types in ascending order; string IDs keep PubChem's order.
- `pubchem_get_summary`: Get descriptive summaries for PubChem entities by ID. Supports assays (AID), genes (Gene ID), proteins (UniProt accession), and taxonomy (Tax ID). Up to 10 per call; identifiers past that are returned in unprocessed for a follow-up call.
- `pubchem_search_assays`: Find PubChem bioassays associated with a biological target. Search by gene symbol (e.g. "EGFR"), protein name, NCBI Gene ID, or UniProt accession. Returns a page of assay IDs (AIDs) — page past maxResults with offset — which can be explored further with pubchem_get_summary.
- `pubchem_search_compounds`: Search PubChem for chemical compounds by identifier (name, SMILES, or InChIKey, up to 25 per call), molecular formula in Hill notation, substructure or superstructure containment, 2D Tanimoto similarity, or the compounds a bioassay (AID) found active or tested. Returns a page of CIDs — reach matches past maxResults with offset. Optionally hydrate results with properties to avoid a follow-up pubchem_get_compound_details call.