PDBe MCP Servers

Access Protein Data Bank in Europe (PDBe) structural biology data from any AI client that supports the Model Context Protocol (MCP).

Capabilities

Molecular workspace (MCP Apps)

In an MCP Apps client, the Apps server provides a shared Mol* workspace for:

• Structure Explorer: inspect chains, residues, ligand instances, and source annotations, with linked sequence and annotation tracks.
• Ligand & Binding Site Explorer: inspect PDBe-reported ligand interaction records, filter evidence, and export contacts.
• Structure Comparison: view PDBe's precomputed superpositions and PDBe/SIFTS residue correspondence, with a correspondence table and CSV export.
• MolViewSpec Builder and Stories: create custom scenes and ordered multi-scene molecular stories.
• Workspace management: save or restore workspace JSON, export MVSJ, and update scenes and layers through MCP tools.

Use pdbe_apps_server for the dedicated server or the recommended all server; connection examples are below. The host needs MCP Apps support, WebGL, and access to https://www.ebi.ac.uk. Clients without UI support receive text and structured data fallbacks.

Comparisons use supplied PDBe transforms and mappings; the app does not calculate a new fit, RMSD, or proximity-derived binding sites. The ligand explorer displays PDBe-supplied interaction records rather than calculating new contacts. Chain selectors use label chain IDs (struct_asym_id).

Example prompts for an MCP Apps-capable client:

• “Open PDB entry 1tqn in the molecular workspace.”
• “Compare the alpha chains of human deoxy- and oxyhemoglobin (PDB 4hhb and 1hho) and show their residue correspondence.”
• “Explore a ligand in PDB entry 1tqn and show its PDBe-reported interactions.”
• “Build a two-scene molecular story for PDB entry 1tqn, showing the protein first and then highlighting a ligand.”

See the molecular workspace guide for setup, tool examples, annotations, saved workspaces, updates, and host routing. The Apps and aggregate servers also expose the molview-spec skill as MCP resources for scene-building guidance.

Data servers

Server	Purpose
all	API, Search, Apps, and Graph tools through one server
pdbe_api_server	Entries, assemblies, molecules, ligands, publications, and validation data
pdbe_search_server	Solr searches with filtering, facets, grouping, and pagination
pdbe_apps_server	Interactive structure and ligand exploration, comparison, and MolViewSpec workspaces
pdbe_graph_server	PDBe-KB graph schema and queries against your local Neo4j database

The recommended all server exposes API, Search, Apps, and Graph together. Graph queries require your own PDBe-KB Neo4j database; PDBe does not provide a public running instance. Configure individual server types if you only need a subset of the tools.

Quick start

Requires Python 3.11+ and uv. Run directly from PyPI without a separate installation:

uvx pdbe-mcp-server

With no server type specified, this starts the aggregate all server over stdio. To run only Search instead:

uvx pdbe-mcp-server --server-type pdbe_search_server

Connect your AI client

For clients using a JSON mcpServers configuration, we recommend starting with the aggregate server. It exposes the API, Search, Apps, and Graph tools through one stdio connection:

{
  "mcpServers": {
    "PDBe": {
      "command": "uvx",
      "args": ["pdbe-mcp-server", "--server-type", "all"]
    }
  }
}

Graph queries require your own PDBe-KB Neo4j database, and interactive Apps views require an Apps-capable client.

If you only need selected servers, configure one or more individually:

{
  "mcpServers": {
    "PDBe API": {
      "command": "uvx",
      "args": ["pdbe-mcp-server", "--server-type", "pdbe_api_server"]
    },
    "PDBe Search": {
      "command": "uvx",
      "args": ["pdbe-mcp-server", "--server-type", "pdbe_search_server"]
    }
  }
}

Ensure uvx is in your client's PATH, then restart or reload the client. Clients with a settings UI can use the same commands and arguments.

Try asking:

• “Find structures for UniProt accession P12345.”
• “Show structures released this month, grouped by experimental method.”
• “Find X-ray structures with resolution better than 2.0 Å.”

See worked examples for questions involving protein function, ligand interactions, glycosylation, cryo-EM structures, and EMDB maps.

Remote HTTP server

From a local checkout, start Streamable HTTP with:

uv run pdbe-mcp-remote-server --all

Connect to http://127.0.0.1:8000/api/, /search/, /apps/, or /graph/. The --all flag also exposes /all/. Use ROOT_PREFIX for a path prefix.

See the server reference for Docker, legacy SSE, search parameters, graph setup, and TOON output configuration.

PDBe-hosted beta server

A beta-hosted remote MCP server is available at https://wwwdev.ebi.ac.uk/pdbe/mcp/all/. Connect to it from an MCP client using Streamable HTTP. As a beta service, its availability and interface may change. For beta-server issues or feedback, email pdbehelp@ebi.ac.uk. For other issues, please open a GitHub issue.

Local development

Clone the repository and install dependencies:

git clone https://github.com/PDBeurope/PDBe-MCP-Servers.git
cd PDBe-MCP-Servers
uv sync --all-extras --dev

Build the molecular UI with Node.js 22.12+ before running the Apps server or building a Python distribution:

cd apps/structure-explorer
npm ci
npm run build
cd ../..

For a local client connection, replace uvx with uv and use arguments like:

["run", "--directory", "/path/to/PDBe-MCP-Servers", "pdbe-mcp-server", "--server-type", "pdbe_api_server"]

Rebuild the UI after UI changes. Python distributions include the generated HTML artifacts. See Development for testing and packaging, and Contributing for contribution guidance.

Documentation and support

• Molecular workspace guide
• Server and tool reference
• Worked examples
• PDBe API documentation
• PDBe-KB graph documentation
• Model Context Protocol
• GitHub issues
• PDBe Help & Support

Licensed under Apache 2.0.