How do I install the pdbe mcp servers 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 `NEO4J_URL`, `NEO4J_USERNAME`, `NEO4J_PASSWORD` 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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PDBe MCP Servers

PDBe MCP Servers (Official) from the PDBe team integrate Protein Data Bank Europe resources with LLMs via Model Context Protocol. Provides seamless

Local serverstdioPython

What is the PDBe MCP Servers?

PDBe MCP Servers (Official) from the PDBe team integrate Protein Data Bank Europe resources with LLMs via Model Context Protocol. Provides seamless access to

Configuration and credentials

Python 3.10+ - Required for the server runtime - uv - Fast Python package manager and dependency resolver

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
get_pdbe_search_schema	Retrieves the complete Solr search schema showing all available fields, data types, and descriptions. Use this to understand what fields you can search and filter on.
run_pdbe_search_query	Execute Solr-style search queries with flexible field selection, filter queries, facets, grouping, sorting, and pagination options.
pdbe_graph_nodes	Retrieves metadata about all node types (labels) defined in the PDBe graph database schema. This uses the public graph schema and does not require local Neo4j credentials.
pdbe_graph_edges	Retrieves metadata about all relationship types (edges) defined in the PDBe graph database schema. This uses the public graph schema and does not require local Neo4j credentials.
pdbe_graph_node_relationships	Verifies selected node labels and returns the incoming, outgoing, and self-loop relationship patterns defined for each label. This uses the public graph schema and does not require local Neo4j credentials.
pdbe_graph_example_queries	Retrieves example Cypher queries that demonstrate how to interact with the PDBe graph database. This uses the public graph schema and does not require local Neo4j credentials.
pdbe_run_cypher_query	Execute custom read-only Cypher queries against your configured Neo4j graph database. This tool is only available when Neo4j environment variables are configured.

How to install the PDBe MCP Servers

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

Configuration as documented by the project. Restart the client after saving.

Configuration

Python 3.10+ - Required for the server runtime - uv - Fast Python package manager and dependency resolver

Variable	Description	Required
NEO4J_URL	Endpoint or connection string the server talks to.	Yes
NEO4J_USERNAME	Configuration value read at startup.	Optional
NEO4J_PASSWORD	Configuration value read at startup.	Optional

Example prompts to try

“Use PDBe MCP Servers to Configuration.”
“Use PDBe MCP Servers to get pdbe search schema.”
“Use PDBe MCP Servers to run pdbe search query.”

Frequently asked questions

PDBe MCP Servers (Official) from the PDBe team integrate Protein Data Bank Europe resources with LLMs via Model Context Protocol. Provides seamless access to Confirm the tools offered by your installed version in the connected client. Tool availability and permissions depend on the server and account configuration.