GlyGen MCP Server

Remote MCP server maintained by the GlyGen project that exposes its integrated carbohydrate and glycoconjugate knowledgebase — glycans, glycoproteins, glycosylation sites, biomarkers, and disease associations — to Claude.

   
Type MCP server (remote, streamable HTTP)
Supplier GlyGen
Availability Beta — remote endpoint live; source repo glygener/glygen-mcp-server last updated 2026-06-25
Pricing Unverified — GlyGen data is freely accessible, but the MCP wrapper repo declares no LICENSE file, so redistribution terms are unstated
Capabilities Read-only — data lookup/summary queries
Verified degraded · 2026-07-20 — self-host repo current but hosted endpoint returned 503 this run
Security caution · 2026-07-20 — provenance matches GlyGen but wrapper repo has no LICENSE, single-maintainer

How to install

  • Claude.ai — Settings → Connectors → Add custom connector. Name it Glygen MCP Server, server URL https://mcp.glygen.org/mcp. (Team/Enterprise: an admin adds it under Admin settings → Connectors.)
  • Claude Code — direct remote MCP add: 
    claude mcp add --transport http glygen https://mcp.glygen.org/mcp

    This is a long-lived hosted service — nothing to run locally. After adding, run /mcp to confirm the server is connected.

  • Claude Desktop — Claude Desktop has no native HTTP transport, so register the remote endpoint through the mcp-remote proxy in claude_desktop_config.json: 
    {
  "mcpServers": {
    "glygen": {
      "command": "npx",
      "args": ["-y", "mcp-remote", "https://mcp.glygen.org/mcp"]
    }
  }
}

    (Requires Node.js so npx is available.)

  • Self-host (optional) — clone glygener/glygen-mcp-server and build the Docker container with python3 create_mcp_container.py -s dev (Linux VM; the README documents a systemd unit for persistence). Only needed if you want to run your own instance rather than use the hosted endpoint above.

What it does

Five read-only summary tools over GlyGen’s integrated datasets:

  • get_protein_summary — glycoprotein record summary (keyed by UniProt accession)
  • get_site_summary — glycosylation site details for a protein
  • get_glycan_summary — glycan structure/composition record (GlyTouCan-linked)
  • get_biomarker_summary — biomarker record summary
  • get_disease_summary — disease association summary

GlyGen integrates and harmonizes carbohydrate/glycoconjugate data from UniProtKB, GlyTouCan, UniCarbKB, and other international sources.

Primary use cases: Glycan and glycoprotein lookup, glycosylation-site queries, glycan-disease/biomarker association retrieval.

Notes

Remote streamable-HTTP endpoint (https://mcp.glygen.org/mcp); no API key documented. GlyGen also exposes a REST API (api.glygen.org) and a SPARQL endpoint (sparql.glygen.org) for programmatic access outside Claude.

License caveat: the glygen-mcp-server GitHub repo has no LICENSE file (the GitHub license field is null as of 2026-07-15), so the redistribution terms of the wrapper are unverified — pricing above reflects this rather than asserting Free / OSS. The underlying GlyGen data is publicly and freely accessible.

Surfaced from user request #48 (@goodb). The request suggested the General-Purpose Utilities shelf, but GlyGen is a life-science data resource spanning glycochemistry, glycobiology, and biomarker/disease data, so it is tagged All.

Sources

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