# pubchem-mcp-server [Health: Active] **Category:** 🧬 Biology & Bioinformatics **Repository:** https://github.com/cyanheads/pubchem-mcp-server **GitHub Stars:** 9 **Views:** 0 **Installs:** 0 **Upvotes:** 0 **Directory Page:** https://allmcps.com/mcp/pubchem-mcp-server ## Description MCP server for PubChem. Search compounds, properties, safety, bioactivity, xrefs, and summaries. ## Claude Desktop Quick Installation Install path detected from listing signals. Uses `bunx` (confidence: high): ```json "mcpServers": { "pubchem-mcp-server": { "command": "bunx", "args": ["@cyanheads/pubchem-mcp-server@latest"] } } ``` ## Documentation & README

@cyanheads/pubchem-mcp-server

Search the PubChem chemical database for compounds, properties, safety data, bioactivity, cross-references, and entity summaries via MCP. STDIO or Streamable HTTP.

10 Tools • 6 Resources

[![Version](https://img.shields.io/badge/Version-0.6.1-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/pubchem-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^2.0.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/pubchem-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubchem-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-^1.3.0-f472b6.svg?style=flat-square)](https://bun.sh/)
[![Install in Claude Desktop](https://img.shields.io/badge/Install_in-Claude_Desktop-D97757?style=for-the-badge&logo=anthropic&logoColor=white)](https://github.com/cyanheads/pubchem-mcp-server/releases/latest/download/pubchem-mcp-server.mcpb) [![Install in Cursor](https://cursor.com/deeplink/mcp-install-dark.svg)](https://cursor.com/en/install-mcp?name=pubchem-mcp-server&config=eyJjb21tYW5kIjoibnB4IiwiYXJncyI6WyIteSIsIkBjeWFuaGVhZHMvcHViY2hlbS1tY3Atc2VydmVyIl19) [![Install in VS Code](https://img.shields.io/badge/VS_Code-Install_Server-0098FF?style=for-the-badge&logo=visualstudiocode&logoColor=white)](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) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-67E8F9?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
**Public Hosted Server:** [https://pubchem.caseyjhand.com/mcp](https://pubchem.caseyjhand.com/mcp)
--- ## 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`](https://github.com/cyanheads/pubchem-mcp-server/blob/HEAD/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](https://github.com/cyanheads/pubchem-mcp-server/blob/HEAD/LICENSE) for details.