io.github.cyanheads/pubchem-mcp-server
Search PubChem compounds, properties, safety data, bioactivity, and cross-references.
Open source Repository Open in the app JSON README (API)
About
Search PubChem compounds, properties, safety data, bioactivity, and cross-references.
Details
- Kind
- MCP servers
- Topic
- No topic detected
- Publisher
- cyanheads
- Origin
- official
- Category
- ferramentas
- Transport
- http
- Version
- 0.6.1
- Stars
- 9
- Forks
- 3
- Last push
- 2026-08-21T22:48:56Z
- Repository state
- ativo
- Language
- TypeScript
- License
- Apache-2.0
- Added
- 2026-08-29 03:02:39
- Updated
- 2026-08-29 03:02:39
- Origin id
io.github.cyanheads/pubchem-mcp-server
README
<div align="center">
<h1>@cyanheads/pubchem-mcp-server</h1>
<p><b>Search the PubChem chemical database for compounds, properties, safety data, bioactivity, cross-references, and entity summaries via MCP. STDIO or Streamable HTTP.</b>
<div>10 Tools • 6 Resources</div>
</p>
</div>
<div align="center">
[](./CHANGELOG.md) [](./LICENSE) [](https://github.com/users/cyanheads/packages/container/package/pubchem-mcp-server) [](https://modelcontextprotocol.io/) [](https://www.npmjs.com/package/@cyanheads/pubchem-mcp-server) [](https://www.typescriptlang.org/) [](https://bun.sh/)
</div>
<div align="center">
[](https://github.com/cyanheads/pubchem-mcp-server/releases/latest/download/pubchem-mcp-server.mcpb) [](https://cursor.com/en/install-mcp?name=pubchem-mcp-server&config=eyJjb21tYW5kIjoibnB4IiwiYXJncyI6WyIteSIsIkBjeWFuaGVhZHMvcHViY2hlbS1tY3Atc2VydmVyIl19) [](https://vscode.dev/redirect?url=vscode:mcp/install?%7B%22name%22%3A%22pubchem-mcp-server%22%2C%22command%22%3A%22npx%22%2C%22args%22%3A%5B%22-y%22%2C%22%40cyanheads/pubchem-mcp-server%22%5D%7D)
[](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
</div>
<div align="center">
**Public Hosted Server:** [https://pubchem.caseyjhand.com/mcp](https://pubchem.caseyjhand.com/mcp)
</div>
---
## Tools
Ten tools for querying PubChem's chemical information database:
| Tool Name | Description |
|:----------|:------------|
| `pubchem_search_compounds` | Search for compounds by name, SMILES, InChIKey, formula, substructure, superstructure, or 2D similarity. |
| `pubchem_get_compound_details` | Get physicochemical properties, descriptions, synonyms, drug-likeness, and classification for compounds by CID. |
| `pubchem_get_compound_image` | Fetch a 2D structure diagram (PNG) for a compound by CID. |
| `pubchem_get_compound_3d_structure` | Fetch a 3D conformer (atomic coordinates and bonds) for a compound by CID, as parsed JSON or raw SDF. |
| `pubchem_get_compound_xrefs` | Get external database cross-references (PubMed, patents, genes, proteins, etc.). |
| `pubchem_get_compound_safety` | Get GHS hazard classification and safety data for one or more compounds by CID (batch). |
| `pubchem_get_bioactivity` | Get a compound's bioactivity profile: assay results, targets, and activity values; filter by outcome or molecular target. |
| `pubchem_get_compound_interactions` | Get drug-drug, drug-food, and chemical-target interactions for a compound by CID. |
| `pubchem_search_assays` | Find bioassays by biological target (gene symbol, protein, Gene ID, UniProt accession). |
| `pubchem_get_summary` | Get summaries for PubChem entities: assays, genes, proteins, taxonomy. |
### `pubchem_search_compounds`
Search PubChem for chemical compounds across five search modes.
- **Identifier lookup** — resolve compound names, SMILES, or InChIKeys to CIDs (batch up to 25)
- **Formula search** — find compounds by molecular formula in Hill notation
- **Substructure/superstructure** — find compounds containing or contained within a query structure
- **2D similarity** — find structurally similar compounds by Tanimoto similarity (configurable threshold)
- Caps at 200 CIDs per page; `offset` pages further, to a ceiling of 10,000. Identifier lookups page over the set already resolved; formula and structure searches widen their bounded upstream request to reach a page, so deep pages cost more upstream
- Optionally hydrate results with properties to avoid a follow-up details call
---
### `pubchem_get_compound_details`
Get detailed compound information by CID.
- Batches up to 100 CIDs in a single request
- 27 available properties: molecular weight, SMILES, InChIKey, XLogP, TPSA, complexity, stereo counts, and more
- Optionally includes textual descriptions (pharmacology, mechanism, therapeutic use) from PUG View — fetched for the first 10 CIDs of a batch, with the skipped CIDs named in the response
- Optionally includes known synonyms (trade names, systematic names, registry numbers)
- Synonyms and descriptions are paged: `synonymOffset` and `descriptionOffset` window every compound in the batch at the same position, reaching the entries past a page
- Optionally computes drug-likeness assessment (Lipinski Rule of Five + Veber rules) from fetched properties
- Optionally fetches pharmacological classification (FDA classes, mechanisms of action, MeSH classes, ATC codes)
---
### `pubchem_get_bioactivity`
Get a compound's bioactivity profile from PubChem BioAssay.
- Returns assay outcomes (Active/Inactive/Inconclusive), target info (protein accessions, NCBI Gene IDs), and quantitative values (IC50, EC50, Ki)
- Filter by outcome and/or a specific molecular target (NCBI Gene ID or protein accession)
- Caps at 100 results per page; `offset` reaches the rest (well-studied compounds may have thousands)
---
### `pubchem_get_summary`
Get descriptive summaries for four PubChem entity types.
- Assays (AID), genes (Gene ID), proteins (UniProt accession), taxonomy (Tax ID)
- Up to 10 entities per call
- Type-specific field extraction for clean, structured output
---
### `pubchem_get_compound_interactions`
Get a compound's interaction data by CID.
- Drug-drug interactions (DrugBank), drug-food interactions, and chemical-target binding/activity (BindingDB, ChEMBL, and others)
- Select which interaction kinds to fetch and cap entries per kind
- Paged per kind: each reports its source-record total and its own `nextOffset`, and `offset` reaches the records past a page
- Each entry carries its originating source — coverage is richest for approved drugs
---
### `pubchem_get_compound_3d_structure`
Get a compound's default 3D conformer by CID.
- `format="json"` returns parsed atoms (element + x/y/z) and bonds for direct reasoning; `format="sdf"` returns raw V2000 SDF for passthrough to docking or rendering
- `maxAtoms`/`maxBonds` bound the atom/bond preview and `includeRawSdf` opts into a large raw SDF past the safe line cap; `atomCount`/`bondCount` always report the totals and any capping is disclosed
- Optionally lists alternate conformer IDs
- Returns a typed not-found when PubChem has no computed 3D coordinates (large molecules, mixtures, some salts)
## Resources
Compound and assay records are also exposed as URI-templated MCP resources, backed by the same client methods as the tools:
| URI Template | Returns |
|:-------------|:--------|
| `pubchem://compound/{cid}` | Core physicochemical properties (JSON). |
| `pubchem://compound/{cid}/safety` | GHS hazard classification (JSON). |
| `pubchem://compound/{cid}/image` | 2D structure diagram (PNG). |
| `pubchem://compound/{cid}/xrefs` | External cross-references (JSON). |
| `pubchem://compound/{cid}/bioactivity` | Bioassay activity profile (JSON). |
| `pubchem://assay/{aid}` | BioAssay summary (JSON). |
## Features
Built on [`@cyanheads/mcp-ts-core`](https://github.com/cyanheads/mcp-ts-core):
- Declarative tool definitions — single file per tool, framework handles registration and validation
- Unified error handling across all tools
- Pluggable auth (`none`, `jwt`, `oauth`)
- Swappable storage backends: `in-memory`, `filesystem`, `Supabase`, `Cloudflare KV/R2/D1`
- Structured logging with optional OpenTelemetry tracing
- Runs locally (stdio/HTTP) or containerized via Docker
PubChem-specific:
- Rate-limited client for PUG REST and PUG View APIs (5 req/s with automatic queuing)
- Retry with exponential backoff on 5xx errors and network failures
- All tools are read-only and idempotent — no API keys required
## Getting Started
### Public Hosted Instance
A public instance is available at `https://pubchem.caseyjhand.com/mcp` — no installation required. Point any MCP client at it via Streamable HTTP:
```json
{
"mcpServers": {
"pubchem-mcp-server": {
"type": "streamable-http",
"url": "https://pubchem.caseyjhand.com/mcp"
}
}
}
```
### Self-Hosted / Local
Add to your MCP client config (e.g., `claude_desktop_config.json`):
```json
{
"mcpServers": {
"pubchem-mcp-server": {
"type": "stdio",
"command": "bunx",
"args": ["@cyanheads/pubchem-mcp-server@latest"],
"env": {
"MCP_TRANSPORT_TYPE": "stdio"
}
}
}
}
```
### Prerequisites
- [Bun v1.3.0](https://bun.sh/) or higher (or Node.js v24+)
### Installation
1. **Clone the repository:**
```sh
git clone https://github.com/cyanheads/pubchem-mcp-server.git
```
1. **Navigate into the directory:**
```sh
cd pubchem-mcp-server
```
1. **Install dependencies:**
```sh
bun install
```
## Configuration
No API keys are required — PubChem's API is freely accessible.
| Variable | Description | Default |
|:---------|:------------|:--------|
| `MCP_TRANSPORT_TYPE` | Transport: `stdio` or `http`. | `stdio` |
| `MCP_HTTP_PORT` | Port for HTTP server. | `3010` |
| `MCP_HTTP_HOST` | Host for HTTP server. | `localhost` |
| `MCP_AUTH_MODE` | Auth mode: `none`, `jwt`, or `oauth`. | `none` |
| `MCP_LOG_LEVEL` | Log level (RFC 5424). | `info` |
| `STORAGE_PROVIDER_TYPE` | Storage backend. | `in-memory` |
| `OTEL_ENABLED` | Enable OpenTelemetry. | `false` |
## Running the Server
### Local Development
- **Build and run:**
```sh
bun run rebuild
bun run start:stdio # or start:http
```
- **Run checks and tests:**
```sh
bun run devcheck # Lints, formats, type-checks
bun run test # Runs test suite
```
### Docker
```sh
docker build -t pubchem-mcp-server .
docker run -p 3010:3010 pubchem-mcp-server
```
## Project Structure
| Directory | Purpose |
|:----------|:--------|
| `src/mcp-server/tools/definitions/` | Tool definitions (`*.tool.ts`). |
| `src/services/pubchem/` | PubChem API client with rate limiting and response parsing. |
| `scripts/` | Build, clean, devcheck, and tree generation scripts. |
## Development Guide
See [`CLAUDE.md`](./CLAUDE.md) for development guidelines and architectural rules. The short version:
- Handlers throw, framework catches — no `try/catch` in tool logic
- Use `ctx.log` for domain-specific logging
- Register new tools in the `index.ts` barrel file
## Contributing
Issues and pull requests are welcome. Run checks before submitting:
```sh
bun run devcheck
bun run test
```
## License
Apache-2.0 — see [LICENSE](LICENSE) for details.