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STDIO or Streamable HTTP.","maintainers":[{"name":"cyanheads","email":"casey@caseyjhand.com"}],"readme":"
\n

@cyanheads/protein-mcp-server

\n

Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models via MCP. STDIO or Streamable HTTP.\n

7 Tools • 2 Resources
\n

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\n\n[![Version](https://img.shields.io/badge/Version-0.8.5-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/protein-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/protein-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/protein-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-v1.4.0%2B-blueviolet.svg?style=flat-square)](https://bun.sh/)\n\n
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\n\n[![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/protein-mcp-server/releases/latest/download/protein-mcp-server.mcpb) [![Install in Cursor](https://cursor.com/deeplink/mcp-install-dark.svg)](https://cursor.com/en/install-mcp?name=protein-mcp-server&config=eyJjb21tYW5kIjoibnB4IiwiYXJncyI6WyIteSIsIkBjeWFuaGVhZHMvcHJvdGVpbi1tY3Atc2VydmVyIl19) [![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%22protein-mcp-server%22%2C%22command%22%3A%22npx%22%2C%22args%22%3A%5B%22-y%22%2C%22%40cyanheads%2Fprotein-mcp-server%22%5D%7D)\n\n[![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)\n\n
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\n\n**Public Hosted Server:** [https://protein.caseyjhand.com/mcp](https://protein.caseyjhand.com/mcp)\n\n
\n\n---\n\n## Overview\n\nExperimental (PDB) and predicted (AlphaFold) protein structures, federated behind one surface. Search, fetch, align, compare, and annotate structures and their ligands across RCSB, AlphaFold DB, 3D-Beacons, UniProt, InterPro, and Foldseek — all keyless. Runs as a stdio process, a local Streamable HTTP server, or the public hosted endpoint above.\n\n### Tools\n\n| Tool | Description |\n|:---|:---|\n| `protein_search_structures` | Search experimental and predicted structures by free text, sequence, or organism/method/resolution filters, with optional facet breakdowns. |\n| `protein_get_structure` | Fetch metadata and coordinate-file URLs by ID — experimental (PDB), predicted (AlphaFold), or best-available — with batch partial success and optional coordinate inlining. |\n| `protein_find_similar` | Find sequence homologs (RCSB mmseqs2) or fold homologs (Foldseek) from a sequence, PDB ID, or UniProt accession. |\n| `protein_track_ligands` | Resolve ligand names/formulas to component IDs, find structures containing a ligand, or map binding-site residues. |\n| `protein_compare_structures` | Structurally align multiple structures (TM-align / jFATCAT) to a reference or as a full pairwise matrix. |\n| `protein_analyze_collection` | Profile the PDB into distributions and trends with server-side facets — counts, histograms, timelines, and cross-tabs. |\n| `protein_get_annotations` | Fetch UniProt features and natural variants plus InterPro domain/family memberships with GO terms. |\n\n### Resources\n\n| Resource | Description |\n|:---|:---|\n| `pdb://{entry_id}` | Experimental structure summary for a PDB entry — title, method, resolution, organism, bound ligands, and per-entity chain IDs in both the author (`authAsymIds`) and mmCIF label (`labelAsymIds`) namespaces. |\n| `af://{uniprot}` | Predicted-structure summary for a UniProt accession from AlphaFold DB — mean pLDDT, confidence-band fractions, model URLs, and version. |\n\nAll resource data is also reachable via tools — `pdb://{entry_id}` mirrors `protein_get_structure` for `source: experimental`, and `af://{uniprot}` mirrors it for `source: predicted`. Many MCP clients are tool-only and don't surface resources; the summaries remain reachable through the tools.\n\n## Capability reference\n\n### `protein_search_structures` tool\n\n- Free-text, protein-sequence (triggers an mmseqs2 similarity search), and organism / method / resolution filters\n- `content_type` scopes the search to `experimental`, `predicted`, or `all` (default) — `all` is a genuine union, so computed models appear alongside PDB entries\n- Every hit names its `source`; sequence hits in either universe expose a chainable entry `id` plus the matched polymer `entityId`; experimental hits carry title, method, resolution, and organism enrichment, and AlphaFold models their parsed UniProt accession\n- `start` and `limit` page through ranked results; `nextStart` is returned while another page remains, and an empty page past the end names the offset in `notice` rather than reporting no matches\n- Optional `facets` return a method / organism / release-year breakdown alongside the hits — each dimension may be listed once and reports how many matches carry no value for it; a capped dimension is named in `notice`, with `protein_analyze_collection` (larger `bucket_limit`) as the route to the long tail\n- Chain hit IDs straight into `protein_get_structure`\n\n---\n\n### `protein_get_structure` tool\n\n- `source: experimental` batches PDB entry IDs (also resolving computed-model IDs like `AF_*`/`MA_*` from search, tagged `source: predicted` with their provider); `source: predicted` takes UniProt accessions for AlphaFold models with pLDDT/PAE; `source: best_available` takes UniProt accessions and returns the top federated model (highest-resolution experimental if one exists, else the best prediction)\n- Per-ID partial success — unresolved IDs land in `failed[]`; `requested`/`processed` disclose IDs dropped beyond the batch cap, and every advisory (cap, failure, overflow) joins into one `notice`\n- Records fetched with `source: experimental`, computed models included, also carry `polymerEntities` (both `authAsymIds` and `labelAsymIds`), `ligands`, `molecularWeight`, and `releaseDate`\n- `coordinateUrls` lists only files that exist: BinaryCIF comes from RCSB's ModelServer, the PDB format is omitted for large mmCIF-only entries, and a computed model's files come from its provider (all three formats from AlphaFold DB, mmCIF from ModelArchive) — an AlphaFold model whose provider lookup fails keeps only its RCSB BinaryCIF, named in `notice`\n- `include_coords` inlines coordinate content, subject to a response budget — an over-budget batch returns a per-structure size outline (re-call with `sections: [ids]`), and a single oversized file is withheld with a pointer to its `coordinateUrls`\n- Every response carries an `attribution` block naming upstream data licenses and citations\n\n---\n\n### `protein_find_similar` tool\n\n- `by: sequence` runs a synchronous RCSB mmseqs2 search; `by: structure` runs an asynchronous Foldseek search against experimental and predicted databases — query from a raw sequence, a PDB ID, or a UniProt accession\n- Both modes accept `start`/`limit` and report `totalCount`, echoing `start` and returning `nextStart` while another page remains; an empty page past the end names the offset in `notice`, distinct from a search with no matches\n- Foldseek targets default to `pdb100` + `afdb50`; override via `databases` (e.g. `afdb-swissprot`, `BFVD`)\n- An async job that exceeds the poll budget returns `status: computing` with a `ticketId` — re-call with `ticket_id` to resume; a completed structure search returns the same ticket so a new `start` pages the finished job\n- Foldseek searches each chain of a multichain structure as its own query: a structure response covers one query (`query`, 0-based, default `0`) and reports `queryCount`, with a `notice` naming the other queries; pass `query` with `ticket_id` to read another chain's hits from the same job. An out-of-range `query` is rejected (`query_out_of_range`), not answered with an empty list\n- Structure hits are ranked best first by `score` across every searched database (hits without a score last, ties by database then target) before `start`/`limit` paging\n- Each mode reads only its own controls (`sequence`, `max_evalue`, `min_identity` under `by: sequence`; `ticket_id`, `databases`, `query` under `by: structure`) — a field the selected mode can't consume is rejected, not ignored\n- Each hit names the engine and source database it came from\n\n---\n\n### `protein_track_ligands` tool\n\n- `mode: find_ligand` resolves a name or formula to chemical component IDs with formula, weight, SMILES, and InChIKey — ranked by deposition frequency, most-common match first\n- `totalCount` and `candidatesConsidered` report how many components matched and how many were ranked; a broad name whose matches exceed the candidate pool gets a `notice` to narrow the query\n- A formula-shaped `query` matches on exact composition, spaced (`C29 H31 N7 O`) or unspaced; anything else (a component ID included) matches on name and synonyms\n- `mode: structures_with_ligand` returns PDB entries containing a ligand by exact component ID, with `start`/`limit` paging and `nextStart` while another page remains; a page past the end names the offset in `notice` instead of reporting no entries\n- `mode: binding_site` returns the protein residues lining a ligand's pocket in a structure, with contact distances; ligand instances page with `start`/`limit` like `structures_with_ligand`\n- Pocket residues carry both mmCIF label numbering (`asymId`, `seqId`) and author numbering (`authAsymId`, `authSeqId`) — 1IEP's imatinib pocket lists label THR93 as author THR315; the ligand instance reports its own author chain and residue number\n- Binding sites are experimental-only — computed from deposited coordinates; predicted models carry no bound ligands\n\n---\n\n### `protein_compare_structures` tool\n\n- Aligns 2 to the configured cap (default 10, max 25) structures per call, via `tm-align`, `fatcat-rigid`, or `fatcat-flexible`; optional per-structure `chain` restricts the alignment to a single mmCIF label chain\n- `reference: first` aligns every structure to the first; `reference: all_pairs` computes the full pairwise matrix; a structure repeated in `structures[]` is compared once\n- Each pair is an independent async job with per-pair partial success — a pair still computing when the poll budget elapses returns `status: computing` with a job `uuid`; a failed pair degrades only its own row\n- Re-call with a matching `{ a, b, uuid }` entry in `resume[]` to poll a computing pair instead of resubmitting; a resumed pair reports `a`/`b` in the order its job was submitted, whatever the current `structures[]` order, and a resume under a different `method` is rejected\n- Returns TM-score, RMSD, and aligned-residue count per pair, plus each structure's `modeledResidues` and 0–100 `coverage`, ordered `[a, b]`; TM-score is normalized by `a`'s length, so the same pair scores differently when reversed\n\n---\n\n### `protein_analyze_collection` tool\n\n- Group by `method`, `organism`, `polymer_type`, `resolution`, `release_year`, or `molecular_weight`\n- One `group_by` dimension for a breakdown, or two distinct dimensions for a cross-tab (the first nests the second); a repeated dimension is rejected\n- `interval` sets a histogram bin width (a number, for `resolution` or `molecular_weight`) or date-histogram period (`year`, the only one RCSB accepts) — applies to whichever requested dimension can consume that type; rejected when neither can\n- Scope with a free-text `query`, `organism`, `method`, or `max_resolution`; `content_type` selects the structure universe\n- `bucket_limit` caps buckets per dimension level, not per response — a cross-tab applies it separately to the parent and each nested child, up to `bucket_limit × (1 + bucket_limit)` buckets; `notice` names every capped position and `bucketsReturned` gives the realized total\n- Every dimension reports `missingValueCount` — matches carrying no value for that attribute (e.g. a `resolution` breakdown excludes NMR entries; computed models have neither `method` nor `resolution`)\n\n---\n\n### `protein_get_annotations` tool\n\n- UniProt features (domains, binding sites, PTMs) and natural variants, plus InterPro domain/family memberships (Pfam, PROSITE, …) with associated GO terms\n- Provide a UniProt accession directly, or a PDB ID — resolved via the structure's sequence cross-reference\n- A multi-chain PDB entry can map to several accessions; the default is the deterministic lowest-author-chain pick, with alternatives listed under `ambiguity` — pass `chain` (an author chain ID) to select a specific one\n- `include` scopes which classes are fetched (`features`, `domains`, `variants`, `all`); `limit` caps each class independently (1–200, default 50), with a truncated class disclosed in `notice`\n- Every response carries an `attribution` block naming the upstream data licenses and citations (see [Upstream data licensing](#upstream-data-licensing))\n\n---\n\n### `pdb://{entry_id}` resource\n\n- Experimental structure summary as `application/json` — title, method, resolution, organism, bound ligands, and per-entity chain IDs in both the author (`authAsymIds`) and mmCIF label (`labelAsymIds`) namespaces\n- Mirrors `protein_get_structure` for `source: experimental`; `entry_id` is a PDB entry ID (e.g. `4HHB`)\n\n---\n\n### `af://{uniprot}` resource\n\n- Predicted-structure summary as `application/json` — mean pLDDT, confidence-band fractions, model URLs (`cif`/`pdb`/`bcif`), and AlphaFold model version\n- `uniprot` accepts a UniProt accession or an AlphaFold DB entry ID (e.g. `AF-P69905-F1`); mirrors `protein_get_structure` for `source: predicted`\n\n## Features\n\nBuilt 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.\n\nPDB / AlphaFold-specific:\n\n- One federated surface over experimental (PDB) and predicted (AlphaFold / 3D-Beacons) structures — search, fetch, and compare treat both universes the same\n- Keyless across every upstream — RCSB, AlphaFold DB, 3D-Beacons, UniProt, InterPro, and Foldseek, no API keys to provision\n- Corpus analytics run on RCSB's facet engine — distributions, histograms, and cross-tabs come back as compact bucket counts, not the matching entries\n- Async alignment and Foldseek jobs poll within a bounded budget and hand back a job ticket (`ticketId` / per-pair `uuid`) instead of blocking — re-call with `ticket_id` or a `resume[]` entry to poll the same job instead of resubmitting\n\nAgent-friendly output:\n\n- Provenance on every response — each hit carries a `source` (`experimental` / `predicted`), the engine and database that produced it, and effective-query / total-count echoes so agents can reason about coverage\n- Graceful partial failure — batch fetches and pairwise comparisons return per-item rows (`failed[]`, per-pair `status`) instead of failing the whole request, each with actionable recovery text\n- Discriminated output contracts — typed `source` and `status` unions, `computing` results with resume tickets, and budget-overflow outlines let callers branch on data, not string parsing\n\n## Getting started\n\n### Public Hosted Instance\n\nA public instance is available at `https://protein.caseyjhand.com/mcp` — no installation required. Point any MCP client at it via Streamable HTTP:\n\n```json\n{\n \"mcpServers\": {\n \"protein\": {\n \"type\": \"streamable-http\",\n \"url\": \"https://protein.caseyjhand.com/mcp\"\n }\n }\n}\n```\n\n### Self-Hosted / Local\n\nAdd the following to your MCP client configuration file. No API key is required — every upstream provider is keyless.\n\n```json\n{\n \"mcpServers\": {\n \"protein-mcp-server\": {\n \"type\": \"stdio\",\n \"command\": \"bunx\",\n \"args\": [\"@cyanheads/protein-mcp-server@latest\"],\n \"env\": {\n \"MCP_TRANSPORT_TYPE\": \"stdio\",\n \"MCP_LOG_LEVEL\": \"info\"\n }\n }\n }\n}\n```\n\nOr with npx (no Bun required):\n\n```json\n{\n \"mcpServers\": {\n \"protein-mcp-server\": {\n \"type\": \"stdio\",\n \"command\": \"npx\",\n \"args\": [\"-y\", \"@cyanheads/protein-mcp-server@latest\"],\n \"env\": {\n \"MCP_TRANSPORT_TYPE\": \"stdio\",\n \"MCP_LOG_LEVEL\": \"info\"\n }\n }\n }\n}\n```\n\nOr with Docker:\n\n```json\n{\n \"mcpServers\": {\n \"protein-mcp-server\": {\n \"type\": \"stdio\",\n \"command\": \"docker\",\n \"args\": [\"run\", \"-i\", \"--rm\", \"-e\", \"MCP_TRANSPORT_TYPE=stdio\", \"ghcr.io/cyanheads/protein-mcp-server:latest\"]\n }\n }\n}\n```\n\nFor Streamable HTTP, set the transport and start the server:\n\n```sh\nMCP_TRANSPORT_TYPE=http MCP_HTTP_PORT=3010 bun run start:http\n# Server listens at http://localhost:3010/mcp\n```\n\n### Prerequisites\n\n- [Bun v1.4.0](https://bun.sh/) or higher (or Node.js v24+).\n- No accounts or API keys — RCSB, AlphaFold DB, 3D-Beacons, UniProt, InterPro, and Foldseek are all public and keyless.\n\n### Installation\n\n1. **Clone the repository:**\n\n```sh\ngit clone https://github.com/cyanheads/protein-mcp-server.git\n```\n\n2. **Navigate into the directory:**\n\n```sh\ncd protein-mcp-server\n```\n\n3. **Install dependencies:**\n\n```sh\nbun install\n```\n\n## Configuration\n\nAll upstream providers are keyless, so the server runs out of the box with no configuration. Every variable below is optional.\n\n| Variable | Description | Default |\n|:---|:---|:---|\n| `PROTEIN_ASYNC_POLL_TIMEOUT_MS` | Max wall-clock to poll an async job (alignment / Foldseek) before returning a `computing` result. | `30000` |\n| `PROTEIN_MAX_BATCH_IDS` | Cap on IDs accepted by `protein_get_structure` in one batch (1–100). | `25` |\n| `PROTEIN_MAX_COMPARE_STRUCTURES` | Cap on structures per `protein_compare_structures` call (2–25). | `10` |\n| `PROTEIN_FACET_BUCKET_CAP` | Default cap on buckets per `protein_analyze_collection` dimension (1–500). | `50` |\n| `PROTEIN_FANOUT_CONCURRENCY` | Max concurrent upstream requests for per-ID / per-pair fan-out (1–16). | `5` |\n| `RCSB_SEARCH_BASE_URL` | Base URL for the RCSB Search API v2. | `https://search.rcsb.org` |\n| `ALPHAFOLD_BASE_URL` | Base URL for the AlphaFold Protein Structure Database API. | `https://alphafold.ebi.ac.uk` |\n| `FOLDSEEK_BASE_URL` | Base URL for the Foldseek structural-similarity search service. | `https://search.foldseek.com` |\n| `MCP_TRANSPORT_TYPE` | Transport: `stdio` or `http`. | `stdio` |\n| `MCP_HTTP_PORT` | Port for the HTTP server. | `3010` |\n| `MCP_SESSION_MODE` | HTTP session mode: `stateless`, `stateful`, or `auto`. The server declares `stateless` in code; set this to override it. | `stateless` |\n| `MCP_AUTH_MODE` | Auth mode: `none`, `jwt`, or `oauth`. | `none` |\n| `MCP_LOG_LEVEL` | Log level (RFC 5424). | `info` |\n| `OTEL_ENABLED` | Enable [OpenTelemetry instrumentation](https://github.com/cyanheads/mcp-ts-core/tree/main/docs/telemetry). | `false` |\n\nSee [`.env.example`](./.env.example) for the full list of provider base-URL overrides and tuning limits.\n\n## Running the server\n\n### Local development\n\n- **Build and run:**\n\n ```sh\n # One-time build\n bun run rebuild\n\n # Run the built server\n bun run start:stdio\n # or\n bun run start:http\n ```\n\n- **Run checks and tests:**\n\n ```sh\n bun run devcheck # Lint, format, typecheck, security\n bun run test # Vitest test suite\n bun run lint:mcp # Validate MCP definitions against spec\n ```\n\n### Docker\n\n```sh\ndocker build -t protein-mcp-server .\ndocker run --rm -e MCP_TRANSPORT_TYPE=http -p 3010:3010 protein-mcp-server\n```\n\nThe Dockerfile defaults to HTTP transport, stateless session mode, and logs to `/var/log/protein-mcp-server`. OpenTelemetry peer dependencies are installed by default — build with `--build-arg OTEL_ENABLED=false` to omit them.\n\n## Project structure\n\n| Directory | Purpose |\n|:---|:---|\n| `src/index.ts` | `createApp()` entry point — registers tools/resources and inits the provider services. |\n| `src/config` | Server-specific environment variable parsing and validation with Zod. |\n| `src/mcp-server/tools` | Tool definitions (`*.tool.ts`). |\n| `src/mcp-server/resources` | Resource definitions (`*.resource.ts`). |\n| `src/services` | Provider service layer — RCSB (search, data, facets), AlphaFold, 3D-Beacons (best-available), UniProt (incl. InterPro/GO), Structural Comparison alignment, Foldseek, and shared HTTP/identifier/concurrency helpers. |\n| `tests/` | Unit and integration tests mirroring `src/`. |\n\n## Development guide\n\nSee [`CLAUDE.md`/`AGENTS.md`](./CLAUDE.md) for development guidelines and architectural rules. The short version:\n\n- Handlers throw, framework catches — no `try/catch` in tool logic\n- Use `ctx.log` for request-scoped logging, `ctx.state` for tenant-scoped storage\n- Register new tools and resources via the barrels in `src/mcp-server/*/definitions/index.ts`\n- Wrap external API calls: validate raw → normalize to domain type → return output schema; never fabricate missing fields\n\n## Upstream data licensing\n\nStructure and annotation data comes from public upstream databases, each under its own license. `protein_get_structure` and `protein_get_annotations` carry an `attribution` block on every response — the license, citation, and homepage for each source that contributed to that specific response — so the attribution obligation travels with the data to downstream consumers rather than living only here. CC BY / CC BY-SA sources require attribution on redistribution; CC0 sources are citation-only (attribution encouraged, not required).\n\n| Source | Contributes to | License |\n|:---|:---|:---|\n| [RCSB PDB](https://www.rcsb.org/) | `protein_get_structure` — experimental records | CC0 1.0 Universal |\n| [AlphaFold DB](https://alphafold.ebi.ac.uk/) | `protein_get_structure` — predicted models | CC BY 4.0 |\n| [ModelArchive](https://www.modelarchive.org/) | `protein_get_structure` — `MA_*` computed models | CC BY 4.0 |\n| [SWISS-MODEL](https://swissmodel.expasy.org/) | `protein_get_structure` — `best_available` models | CC BY-SA 4.0 |\n| [BFVD](https://bfvd.steineggerlab.workers.dev/) | `protein_get_structure` — `best_available` models | CC BY 4.0 |\n| [UniProt](https://www.uniprot.org/) | `protein_get_annotations` | CC BY 4.0 |\n| [InterPro](https://www.ebi.ac.uk/interpro/) | `protein_get_annotations` — domain/family data | CC0 1.0 Universal |\n| [GO](https://geneontology.org/) | `protein_get_annotations` — GO terms | CC BY 4.0 |\n\n`best_available` federates predicted models through [3D-Beacons](https://3d-beacons.org/), so the `attribution` block credits the actual contributing provider (AlphaFold DB, SWISS-MODEL, BFVD, …); a provider without a curated license entry carries a `See provider terms` fallback pointing back to 3D-Beacons rather than a fabricated license. InterPro's own domain/family classifications are CC0; the GO terms carried alongside them are separately CC BY 4.0, so each is credited independently only when it actually contributes. Full citations for each source travel in the `attribution` block of the relevant tool responses. This covers upstream *data* licensing — the server's own code is licensed separately (see [License](#license)).\n\n## Contributing\n\nIssues are welcome. Run checks and tests before submitting:\n\n```sh\nbun run devcheck\nbun run test\n```\n\n## License\n\nApache-2.0 — see [LICENSE](LICENSE) for details.\n","readmeFilename":"README.md"}