How do I install the protein mcp server?

Use a recorded configuration for your client, replace example credential values and paths, and verify the documented runtime. Restart or reconnect the client, then inspect the available tools.

What credentials does it need?

It reads `MCP_TRANSPORT_TYPE`, `MCP_LOG_LEVEL`, `RCSB_SEARCH_BASE_URL`, `ALPHAFOLD_BASE_URL`, `FOLDSEEK_BASE_URL` from the environment. Store these in your client's env block or a secrets manager — never commit them to a repository — and grant the narrowest scope that still covers your use case.

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Protein MCP Server

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

Remote serverstreamable-httpGo

What is the Protein MCP Server?

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

Configuration and credentials

Bun v1.3.2 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.

More MCP options

Compare MCP servers by category, or browse hosted MCP servers if you prefer an endpoint over a local process.

Maintainer setup documentation.

Recorded tools

Check the linked publisher documentation and your connected client's tool list. Names and availability can vary with the server version and account permissions.

Tool	What it does
protein_search_structures	Search experimental and predicted structures by text, sequence, or organism/method/resolution, with optional facets
protein_get_structure	Fetch metadata and coordinate URLs for experimental, predicted, or best-available structures
protein_find_similar	Find sequence homologs (RCSB mmseqs2) or fold homologs (Foldseek)
protein_track_ligands	Resolve ligands to component IDs, find structures containing one, or map its binding site
protein_compare_structures	Align structures with TM-align or jFATCAT, against a reference or all pairs
protein_analyze_collection	Profile the PDB as counts, histograms, timelines, and cross-tabs
protein_get_annotations	Fetch UniProt features and variants plus InterPro domains with GO terms

How to install the Protein MCP Server

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

From the project documentation. Replace placeholders and example paths before connecting.

Configuration

Bun v1.3.2 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.

Example prompts to try

“Use Protein to protein search structures.”
“Use Protein to protein get structure.”
“Use Protein to protein find similar.”

Frequently asked questions

Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models via MCP. STDIO or Streamable HTTP. Confirm the tools offered by your installed version in the connected client. Tool availability and permissions depend on the server and account configuration.