Protein MCP Server - install, status & alternatives [2026]

01 · Install Protein MCP Server

before you install - you'll need

Set MCP_TRANSPORT_TYPE, MCP_LOG_LEVEL before connecting.

Claude Code

claude mcp add cyanheads-protein-mcp-server -- npx -y protein-mcp-server

Claude Desktop / Cursor / VS Code - add to config

{
  "mcpServers": {
    "cyanheads-protein-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "protein-mcp-server"
      ]
    }
  }
}

Same JSON for Cursor. For VS Code, rename the top-level key from `mcpServers` to `servers`.

Using another client? Same JSON, different key

Claude Desktop · mcpServers

Cursor · mcpServers

VS Code · servers

Windsurf · mcpServers

Zed · context_servers

Cline · mcpServers

Roo Code · mcpServers

Continue · mcpServers

LibreChat · mcpServers

Gemini CLI · mcpServers

Codex CLI · mcp_servers

Full setup guides: every client.

02 · Evidence

Security posture

What to check before giving this server access to your agent - from the registry, GitHub, and our own probes. We don't score safety; we show what's verifiable.

runs as local process (stdio) - runs on your machine with your user's permissions

license Apache-2.0 - declared in the repository

npm package protein-mcp-server - unscoped; check the name against the project README before installing

registry namespace io.github.cyanheads is GitHub-verified and matches the repo owner

03 · What Protein MCP Server can do

Prose above is summarized from the project's README and registry record - no invented capabilities.

What you can build

With this server connected, an agent can search experimental and predicted structures by free text, sequence, or organism/method/resolution filters, with optional facet breakdowns, find sequence homologs (RCSB mmseqs2) or fold homologs (Foldseek) from a sequence, PDB ID, or UniProt accession, and resolve ligand names/formulas to component IDs, find structures containing a ligand, or map binding-site residues.

The 7 tools it gives your agent

Extracted from the project's README - what protein-mcp-server lets an agent do.

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 coordinat
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.

Latest releases

v0.8.1 · 2026-09-16

mcp-ts-core 0.13.2, stateless session mode declared in source · Server declares stateless HTTP session mode in source - an unset MCP_SESSION_MODE now serves stateless instead of falling through to the schema's auto →…

v0.8.0 · 2026-09-09

find_similar paging + mode guard, error reclassification · protein_get_annotations rejects a missing or malformed identifier as InvalidParams (missing_identifier/invalid_accession) instead of NotFound (#46)…

v0.7.0 · 2026-09-09

chain namespace rename, get_structure advisory & overflow fixes · pdb://{entry_id} polymerEntities[].chains renamed to authAsymIds (#45) · protein_get_structure exposes authAsymIds/labelAsymIds and entry detail…

04 · Who maintains Protein MCP Server

protein-mcp-server is maintained by cyanheads. We track 125 MCP servers from cyanheads - 119 actively maintained, 1,816 combined GitHub stars, oldest repo from Dec 2024. Full record: all servers from cyanheads.

05 · Facts

repository: github.com/cyanheads/protein-mcp-server
category: other - ranked #378 of 945 actively-maintained other servers as of 2026-09-18.
release cadence: 10+ releases in the last 90 days (latest 2026-09-16)
registry: io.github.cyanheads/protein-mcp-server (active, first published 2025-10-02 · 23 versions)
packages: npm:protein-mcp-server · npm:protein-mcp-server

06 · Protein MCP Server FAQ

Is Protein MCP Server still maintained?

Yes - as of 2026-09-18, its last commit was 2026-09-16 and it shipped 10+ releases in the last 90 days. We re-verify nightly.

What can Protein MCP Server do?

With this server connected, an agent can search experimental and predicted structures by free text, sequence, or organism/method/resolution filters, with optional facet breakdowns, find sequence homologs (RCSB mmseqs2) or fold homologs (Foldseek) from a sequence, PDB ID, or UniProt accession, and resolve ligand names/formulas to component IDs, find structures containing a ligand, or map binding-site residues.

How do I install Protein MCP Server?

Run `npx -y protein-mcp-server`. The README documents 2 environment variables (MCP_TRANSPORT_TYPE, MCP_LOG_LEVEL) to set first. Set MCP_TRANSPORT_TYPE, MCP_LOG_LEVEL before connecting. You can also paste the ready-made client config above.

Does Protein MCP Server run locally?

Yes - it's a stdio server: it runs on your machine (via npx) with your user's permissions. Your data stays local unless the server itself calls external APIs.

07 · Alternatives to Protein MCP Server

Alternatives to Protein MCP Server

Maintained other servers if Protein MCP Server isn't the fit.

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