interpro-mcp-server
by cyanheads
README.md
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<h1>@cyanheads/interpro-mcp-server</h1>
<p><b>Search InterPro entries, map protein domains and functional sites, and find proteins by domain via MCP. STDIO or Streamable HTTP.</b>
<div>6 Tools</div>
</p>
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[](./CHANGELOG.md) [](./LICENSE) [](https://github.com/users/cyanheads/packages/container/package/interpro-mcp-server) [](https://modelcontextprotocol.io/) [](https://www.npmjs.com/package/@cyanheads/interpro-mcp-server) [](https://www.typescriptlang.org/) [](https://bun.sh/)
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[](https://github.com/cyanheads/interpro-mcp-server/releases/latest/download/interpro-mcp-server.mcpb) [](https://cursor.com/en/install-mcp?name=interpro-mcp-server&config=eyJjb21tYW5kIjoibnB4IiwiYXJncyI6WyIteSIsIkBjeWFuaGVhZHMvaW50ZXJwcm8tbWNwLXNlcnZlciJdfQ==) [](https://vscode.dev/redirect?url=vscode:mcp/install?%7B%22name%22%3A%22interpro-mcp-server%22%2C%22command%22%3A%22npx%22%2C%22args%22%3A%5B%22-y%22%2C%22%40cyanheads%2Finterpro-mcp-server%22%5D%7D)
[](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
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---
## Overview
Protein families, domains, repeats, and functional sites from [InterPro](https://www.ebi.ac.uk/interpro/) and the member databases it integrates (Pfam, PROSITE, SMART, CDD, PANTHER, and others), read through the keyless EMBL-EBI InterPro API. Search entries, read their full metadata, map a UniProt protein's annotations to residue coordinates, walk Pfam, CDD, and PIRSF clans, and find proteins that carry a signature. Runs over STDIO or Streamable HTTP, with no credentials to configure.
### Tools
| Tool | Description |
|:---|:---|
| `interpro_search_entries` | Find InterPro entries or member signatures by text, entry type, GO annotation, or integrating InterPro accession |
| `interpro_get_entry` | Read one entry's description, hierarchy, member signatures, GO terms, literature, cross-references, clan membership, and coverage counters |
| `interpro_get_protein_domains` | Map a UniProt protein's domains, families, repeats, and functional sites to sequence coordinates, optionally at one residue |
| `interpro_get_clan` | Read a Pfam, CDD, or PIRSF set and page through its members, optionally with its relationship graph |
| `interpro_find_proteins_by_domain` | Find UniProt proteins carrying an entry, defaulting to reviewed human proteins |
| `interpro_list_reference` | Decode database slugs, entry types, accession patterns, common taxon IDs, and the current InterPro release |
## Capability reference
### `interpro_search_entries` <sub>tool</sub>
- `sourceDatabase` (default `interpro`) plus optional `query` (1-300 characters), `entryType`, `goTerm` (`GO:0003677` form), `goCategory` (`P`, `F`, `C`), and `integratedInto` (an `IPR` accession, member databases only); no filter is required, so omitting all of them browses the database
- Cursor-paged, `limit` 1-100 (default 20); returns `entries`, `page` (`total`, `returned`, `hasMore`, `nextCursor`), and the applied `query`
---
### `interpro_get_entry` <sub>tool</sub>
- `accession` required; `sourceDatabase` is inferred from standard accession prefixes when omitted. A set accession (`CL…`) fails as `entry_not_found` and points to `interpro_get_clan`
- Wikipedia thumbnails are omitted unless `includeThumbnail: true`, and a notice reports what was left out
- A withdrawn record fails as `entry_withdrawn` with its deletion date and short name
---
### `interpro_get_protein_domains` <sub>tool</sub>
- Canonical six- or ten-character UniProt `accession` (no isoform suffix); optional `residuePosition` (1-based, inclusive) keeps every match with a fragment covering it, with all of that match's fragments intact; `includeExtraFeatures` adds predicted features such as disorder and transmembrane regions
- Large maps arrive in segments of whole matches within a 100,000-byte response budget, following `coverage.nextCursor` until `hasMore` is `false`. The first segment carries the protein metadata, and an empty segment cannot establish that nothing is annotated
- Discontinuous fragments, models, and upstream scores are kept as returned; `residue_out_of_range` and `protein_not_found` are typed failures
---
### `interpro_get_clan` <sub>tool</sub>
- `accession` for a Pfam (`CL0016`), CDD (`cl21453`), or PIRSF (`PIRSF000047`) set, with `sourceDatabase` (`pfam`, `cdd`, `pirsf`) inferred from the prefix; members page by `cursor`, `limit` 1-100 (default 20)
- `includeRelationships: true` adds the relationship graph in slices that fit the response budget; `relationshipsPage.nextOffset` goes back in as `relationshipOffset`, which needs `includeRelationships` set
- `includeThumbnail` works as on `interpro_get_entry`; a missing set is `clan_not_found`
---
### `interpro_find_proteins_by_domain` <sub>tool</sub>
- `accession` plus optional `sourceDatabase`; `taxonId` (NCBI, default `9606`) and `reviewedOnly` (default `true`; `false` covers reviewed and unreviewed proteins) are echoed in `query`
- Cursor-paged, `limit` 1-50 (default 20); each result keeps the protein summary, matched entry locations, and taxon lineage
- No hits is a success with a notice, since the API answers an unknown entry, an unknown taxon, and an empty intersection the same way
---
### `interpro_list_reference` <sub>tool</sub>
- `topic` required: `databases`, `entry_types`, `accession_patterns`, `taxa`, or `release`. The first four are local and make no network call; `taxa` lists common examples, not every taxon
- `release` reads the current InterPro version, date, and per-database entry counts, and fails as `release_changed` if the two upstream responses disagree on the version
## Features
Built on [`@cyanheads/mcp-ts-core`](https://github.com/cyanheads/mcp-ts-core): stdio and Streamable HTTP transports, pluggable auth (`none` / `jwt` / `oauth`), swappable storage (`in-memory`, `filesystem`, `Supabase`, `Cloudflare KV/R2/D1`), structured logging with optional OpenTelemetry tracing.
InterPro-specific:
- 15 database slugs (`interpro`, `pfam`, `prosite`, `profile`, `smart`, `cdd`, `panther`, `cathgene3d`, `ssf`, `ncbifam`, `hamap`, `prints`, `pirsf`, `sfld`, `antifam`) and 11 entry types, with the entry database inferred from standard accession prefixes and conflicting routes rejected locally
- One process-wide request pacer at one upstream request per second, a 50-second budget per tool call covering pacing, retries, and every request, and a 4 MiB cap on upstream responses
- Upstream HTTP/1.1 client that handles the API's bodyless 204 responses, which native `fetch` rejects on Node
- Sparse upstream metadata passes through as `null` or omitted rather than filled in
Agent-friendly output:
- `content[]` carries the complete output as compact JSON plus an index of every URL as a link and every image as an image, so clients that read only one surface get the same data
- Opaque cursors bound to their query, with a notice naming the exact next call whenever a result is partial
- Typed failure reasons (`entry_not_found`, `invalid_cursor`, `upstream_rate_limited`, and others) each paired with a recovery hint
- Coordinates describe sequence annotation, not pathogenicity or clinical significance
## Getting started
Add the following to your MCP client configuration file. No API key is needed.
```json
{
"mcpServers": {
"interpro-mcp-server": {
"type": "stdio",
"command": "bunx",
"args": ["@cyanheads/interpro-mcp-server@latest"],
"env": {
"MCP_TRANSPORT_TYPE": "stdio",
"MCP_LOG_LEVEL": "info"
}
}
}
}
```
Or with npx (no Bun required):
```json
{
"mcpServers": {
"interpro-mcp-server": {
"type": "stdio",
"command": "npx",
"args": ["-y", "@cyanheads/interpro-mcp-server@latest"],
"env": {
"MCP_TRANSPORT_TYPE": "stdio",
"MCP_LOG_LEVEL": "info"
}
}
}
}
```
Or with Docker:
```json
{
"mcpServers": {
"interpro-mcp-server": {
"type": "stdio",
"command": "docker",
"args": ["run", "-i", "--rm", "-e", "MCP_TRANSPORT_TYPE=stdio", "ghcr.io/cyanheads/interpro-mcp-server:latest"]
}
}
}
```
For Streamable HTTP, set the transport and start the server:
```sh
MCP_TRANSPORT_TYPE=http MCP_HTTP_PORT=3010 bun run start:http
# Server listens at http://localhost:3010/mcp
```
### Prerequisites
- [Bun v1.4.0](https://bun.sh/) or higher (or Node.js v24+).
### Installation
1. **Clone the repository:**
```sh
git clone https://github.com/cyanheads/interpro-mcp-server.git
```
2. **Navigate into the directory:**
```sh
cd interpro-mcp-server
```
3. **Install dependencies:**
```sh
bun install
```
4. **Configure environment (optional):**
```sh
cp .env.example .env
```
## Configuration
The server defines no variables of its own; the InterPro API is keyless. These framework variables are the ones most often set:
| Variable | Description | Default |
|:---|:---|:---|
| `MCP_TRANSPORT_TYPE` | Transport: `stdio` or `http`. | `stdio` |
| `MCP_HTTP_PORT` | HTTP server port. | `3010` |
| `MCP_HTTP_HOST` | HTTP server host. | `127.0.0.1` |
| `MCP_HTTP_ENDPOINT_PATH` | HTTP endpoint path. | `/mcp` |
| `MCP_SESSION_MODE` | HTTP session mode: `stateless`, `stateful`, or `auto`. | `stateless` |
| `MCP_AUTH_MODE` | Authentication: `none`, `jwt`, or `oauth`. With auth on, each tool requires its `tool:<tool_name>:read` scope. | `none` |
| `MCP_LOG_LEVEL` | Log level (`debug`, `info`, `notice`, `warning`, `error`). | `info` |
| `LOGS_DIR` | Directory for log files (Node.js only). | `<app-root>/logs` |
| `STORAGE_PROVIDER_TYPE` | Storage backend: `in-memory`, `filesystem`, `supabase`, `cloudflare-kv/r2/d1`. | `in-memory` |
| `OTEL_ENABLED` | Enable [OpenTelemetry](https://github.com/cyanheads/mcp-ts-core/tree/main/docs/telemetry). | `false` |
See [`.env.example`](./.env.example) for the common framework overrides.
## Running the server
### Local development
- **Build and run the production version**:
```sh
# One-time build
bun run rebuild
# Run the built server
bun run start:http
# or
bun run start:stdio
```
- **Run checks and tests**:
```sh
bun run devcheck # Lints, formats, type-checks, and more
bun run test # Runs the test suite
```
## Project structure
| Directory | Purpose |
|:---|:---|
| `src/index.ts` | `createApp()` entry point: registers the tools and starts the InterPro service. |
| `src/mcp-server/tools` | Tool definitions (`*.tool.ts`). Six tools. |
| `src/services/interpro` | InterPro service: HTTP/1.1 adapter, pacer and deadlines, accession routing, cursors, schemas, and the shared result formatter. |
| `tests/` | Unit and integration tests, mirroring the `src/` structure. |
## Development guide
See [`CLAUDE.md`](./CLAUDE.md) for development guidelines and architectural rules. The short version:
- Handlers throw, framework catches, with no `try/catch` in tool logic
- Use `ctx.log` for request-scoped logging
- Register new tools in the `createApp()` array in `src/index.ts`
- Wrap external API calls: validate raw, normalize to the domain type, return the output schema; never fabricate missing fields
## Contributing
Issues are welcome. Run checks and tests before submitting:
```sh
bun run devcheck
bun run test
```
## License
This project is licensed under the Apache 2.0 License. See the [LICENSE](./LICENSE) file for details.
Data comes from InterPro and its member databases through the EMBL-EBI API. Licensing varies by member database, so attribute InterPro and the originating database; see [InterPro's license page](https://interpro-documentation.readthedocs.io/en/latest/license.html) and the [EMBL-EBI terms of use](https://www.ebi.ac.uk/about/terms-of-use/).
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