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.

Capability map

Tools grouped from the project's README - what Protein MCP Server lets an agent do.

Protein

7 tools - e.g. Search experimental and predicted structures by free text, sequence, or organism/method/resolution filters, with optional facet breakdowns.; Fetch metadata and coordinate-file URLs by ID - experimental…

protein_search_structures · protein_get_structure · protein_find_similar · protein_track_ligands · protein_compare_structures · protein_analyze_collection…

Source

1 tool - e.g. predicted takes UniProt accessions and returns the AlphaFold model with pLDDT/PAE confidence

source

other

1 tool - e.g. sequence runs a synchronous RCSB mmseqs2 search; by: structure runs an asynchronous Foldseek search against experimental and predicted databases

by

Mode

1 tool - e.g. find_ligand resolves a name or formula to chemical component IDs with formula, weight, SMILES, and InChIKey

mode

Methods

1 tool - e.g. tm-align, fatcat-rigid, fatcat-flexible

Methods

Reference

1 tool - e.g. first aligns every structure to the first; reference: all_pairs computes the full pairwise matrix

reference

Latest releases

v0.5.1 · 2026-08-17

bucketsReturned enrichment for protein_analyze_collection · protein_analyze_collection reports bucketsReturned, the realized · bucket total across every dimension level (#36) · bucket_limit's per-dimension-level…

v0.5.0 · 2026-08-17

flat facet child, duplicate-dimension guards · protein_analyze_collection's nested cross-tab position (a bucket's · child dimension) is now a single optional child object, replacing the · children[] array that was…

v0.4.2 · 2026-08-17

Foldseek identity scale, predicted-batch resilience, alignment coverage · protein_find_similar: Foldseek identity now returns a 0-1 fraction as declared, not Foldseek raw 0-100 scale (#24) · protein_get_structure /…

04 · Who maintains Protein MCP Server

protein-mcp-server is maintained by cyanheads. We track 125 MCP servers from cyanheads - 124 actively maintained, 1,730 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 #419 of 848 actively-maintained other servers as of 2026-08-25.
release cadence: 10+ releases in the last 90 days (latest 2026-08-17)
registry: io.github.cyanheads/protein-mcp-server (active, first published 2025-10-02 · 17 versions)
packages: npm:protein-mcp-server · npm:protein-mcp-server

06 · Protein MCP Server FAQ

Is Protein MCP Server still maintained?

Yes - as of 2026-08-25, its last commit was 2026-08-17 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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