protein-mcp-server

---

Overview

Experimental (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.

Tools

Tool	Description
protein_search_structures	Search experimental and predicted structures by free text, sequence, or organism/method/resolution filters, with optional facet breakdowns.
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.
protein_find_similar	Find sequence homologs (RCSB mmseqs2) or fold homologs (Foldseek) from a sequence, PDB ID, or UniProt accession.
protein_track_ligands	Resolve ligand names/formulas to component IDs, find structures containing a ligand, or map binding-site residues.
protein_compare_structures	Structurally align multiple structures (TM-align / jFATCAT) to a reference or as a full pairwise matrix.
protein_analyze_collection	Profile the PDB into distributions and trends with server-side facets — counts, histograms, timelines, and cross-tabs.
protein_get_annotations	Fetch UniProt features and natural variants plus InterPro domain/family memberships with GO terms.

Resources

Resource	Description
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.
af://{uniprot}	Predicted-structure summary for a UniProt accession from AlphaFold DB — mean pLDDT, confidence-band fractions, model URLs, and version.

All 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.

Capability reference

protein_search_structures _tool

• Free-text, protein-sequence (triggers an mmseqs2 similarity search), and organism / method / resolution filters
• content_type scopes the search to experimental, predicted, or all (default) — all is a genuine union, so computed models appear alongside PDB entries
• 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
• 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
• 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
• Chain hit IDs straight into protein_get_structure

---

protein_get_structure _tool

• 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)
• 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
• Records fetched with source: experimental, computed models included, also carry polymerEntities (both authAsymIds and labelAsymIds), ligands, molecularWeight, and releaseDate
• 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
• 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
• Every response carries an attribution block naming upstream data licenses and citations

---

protein_find_similar _tool

• 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
• 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
• Foldseek targets default to pdb100 + afdb50; override via databases (e.g. afdb-swissprot, BFVD)
• 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
• 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
• 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
• 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
• Each hit names the engine and source database it came from

---

protein_track_ligands _tool

• 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
• 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
• 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
• 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
• 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
• 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
• Binding sites are experimental-only — computed from deposited coordinates; predicted models carry no bound ligands

---

protein_compare_structures _tool

• 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
• reference: first aligns every structure to the first; reference: all_pairs computes the full pairwise matrix; a structure repeated in structures[] is compared once
• 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
• 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
• 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

---

protein_analyze_collection _tool

• Group by method, organism, polymer_type, resolution, release_year, or molecular_weight
• 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
• 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
• Scope with a free-text query, organism, method, or max_resolution; content_type selects the structure universe
• 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
• 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)

---

protein_get_annotations _tool

• UniProt features (domains, binding sites, PTMs) and natural variants, plus InterPro domain/family memberships (Pfam, PROSITE, …) with associated GO terms
• Provide a UniProt accession directly, or a PDB ID — resolved via the structure's sequence cross-reference
• 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
• 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
• Every response carries an attribution block naming the upstream data licenses and citations (see Upstream data licensing)

---

pdb://{entry_id} _resource

• 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
• Mirrors protein_get_structure for source: experimental; entry_id is a PDB entry ID (e.g. 4HHB)

---

af://{uniprot} _resource

• Predicted-structure summary as application/json — mean pLDDT, confidence-band fractions, model URLs (cif/pdb/bcif), and AlphaFold model version
• uniprot accepts a UniProt accession or an AlphaFold DB entry ID (e.g. AF-P69905-F1); mirrors protein_get_structure for source: predicted

Features

Built on @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.

PDB / AlphaFold-specific:

• One federated surface over experimental (PDB) and predicted (AlphaFold / 3D-Beacons) structures — search, fetch, and compare treat both universes the same
• Keyless across every upstream — RCSB, AlphaFold DB, 3D-Beacons, UniProt, InterPro, and Foldseek, no API keys to provision
• Corpus analytics run on RCSB's facet engine — distributions, histograms, and cross-tabs come back as compact bucket counts, not the matching entries
• 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

Agent-friendly output:

• 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
• 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
• 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

Getting started

Public Hosted Instance

A public instance is available at https://protein.caseyjhand.com/mcp — no installation required. Point any MCP client at it via Streamable HTTP:

{
  "mcpServers": {
    "protein": {
      "type": "streamable-http",
      "url": "https://protein.caseyjhand.com/mcp"
    }
  }
}

Self-Hosted / Local

Add the following to your MCP client configuration file. No API key is required — every upstream provider is keyless.

{
  "mcpServers": {
    "protein-mcp-server": {
      "type": "stdio",
      "command": "bunx",
      "args": ["@cyanheads/protein-mcp-server@latest"],
      "env": {
        "MCP_TRANSPORT_TYPE": "stdio",
        "MCP_LOG_LEVEL": "info"
      }
    }
  }
}

Or with npx (no Bun required):

{
  "mcpServers": {
    "protein-mcp-server": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "@cyanheads/protein-mcp-server@latest"],
      "env": {
        "MCP_TRANSPORT_TYPE": "stdio",
        "MCP_LOG_LEVEL": "info"
      }
    }
  }
}

Or with Docker:

{
  "mcpServers": {
    "protein-mcp-server": {
      "type": "stdio",
      "command": "docker",
      "args": ["run", "-i", "--rm", "-e", "MCP_TRANSPORT_TYPE=stdio", "ghcr.io/cyanheads/protein-mcp-server:latest"]
    }
  }
}

For Streamable HTTP, set the transport and start the server:

MCP_TRANSPORT_TYPE=http MCP_HTTP_PORT=3010 bun run start:http
# Server listens at http://localhost:3010/mcp

Prerequisites

• Bun v1.4.0 or higher (or Node.js v24+).
• No accounts or API keys — RCSB, AlphaFold DB, 3D-Beacons, UniProt, InterPro, and Foldseek are all public and keyless.

Installation

1. Clone the repository:

git clone https://github.com/cyanheads/protein-mcp-server.git

2. Navigate into the directory:

cd protein-mcp-server

3. Install dependencies:

bun install

Configuration

All upstream providers are keyless, so the server runs out of the box with no configuration. Every variable below is optional.

Variable	Description	Default
PROTEIN_ASYNC_POLL_TIMEOUT_MS	Max wall-clock to poll an async job (alignment / Foldseek) before returning a computing result.	30000
PROTEIN_MAX_BATCH_IDS	Cap on IDs accepted by protein_get_structure in one batch (1–100).	25
PROTEIN_MAX_COMPARE_STRUCTURES	Cap on structures per protein_compare_structures call (2–25).	10
PROTEIN_FACET_BUCKET_CAP	Default cap on buckets per protein_analyze_collection dimension (1–500).	50
PROTEIN_FANOUT_CONCURRENCY	Max concurrent upstream requests for per-ID / per-pair fan-out (1–16).	5
RCSB_SEARCH_BASE_URL	Base URL for the RCSB Search API v2.	https://search.rcsb.org
ALPHAFOLD_BASE_URL	Base URL for the AlphaFold Protein Structure Database API.	https://alphafold.ebi.ac.uk
FOLDSEEK_BASE_URL	Base URL for the Foldseek structural-similarity search service.	https://search.foldseek.com
MCP_TRANSPORT_TYPE	Transport: stdio or http.	stdio
MCP_HTTP_PORT	Port for the HTTP server.	3010
MCP_SESSION_MODE	HTTP session mode: stateless, stateful, or auto. The server declares stateless in code; set this to override it.	stateless
MCP_AUTH_MODE	Auth mode: none, jwt, or oauth.	none
MCP_LOG_LEVEL	Log level (RFC 5424).	info
OTEL_ENABLED	Enable OpenTelemetry instrumentation.	false

See .env.example for the full list of provider base-URL overrides and tuning limits.

Running the server

Local development

• Build and run:

  # One-time build
  bun run rebuild
  
  # Run the built server
  bun run start:stdio
  # or
  bun run start:http
  

• Run checks and tests:

  bun run devcheck   # Lint, format, typecheck, security
  bun run test       # Vitest test suite
  bun run lint:mcp   # Validate MCP definitions against spec
  

Docker

docker build -t protein-mcp-server .
docker run --rm -e MCP_TRANSPORT_TYPE=http -p 3010:3010 protein-mcp-server

The 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.

Project structure

Directory	Purpose
src/index.ts	createApp() entry point — registers tools/resources and inits the provider services.
src/config	Server-specific environment variable parsing and validation with Zod.
src/mcp-server/tools	Tool definitions (*.tool.ts).
src/mcp-server/resources	Resource definitions (*.resource.ts).
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.
tests/	Unit and integration tests mirroring src/.

Development guide

See CLAUDE.md/AGENTS.md for development guidelines and architectural rules. The short version:

• Handlers throw, framework catches — no try/catch in tool logic
• Use ctx.log for request-scoped logging, ctx.state for tenant-scoped storage
• Register new tools and resources via the barrels in src/mcp-server/*/definitions/index.ts
• Wrap external API calls: validate raw → normalize to domain type → return output schema; never fabricate missing fields

Upstream data licensing

Structure 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).

Source	Contributes to	License
RCSB PDB	protein_get_structure — experimental records	CC0 1.0 Universal
AlphaFold DB	protein_get_structure — predicted models	CC BY 4.0
ModelArchive	protein_get_structure — MA_* computed models	CC BY 4.0
SWISS-MODEL	protein_get_structure — best_available models	CC BY-SA 4.0
BFVD	protein_get_structure — best_available models	CC BY 4.0
UniProt	protein_get_annotations	CC BY 4.0
InterPro	protein_get_annotations — domain/family data	CC0 1.0 Universal
GO	protein_get_annotations — GO terms	CC BY 4.0

best_available federates predicted models through 3D-Beacons, 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).

Contributing

Issues are welcome. Run checks and tests before submitting:

bun run devcheck
bun run test

License

Apache-2.0 — see LICENSE for details.