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 use it
Project documentation lists pdbe_run_cypher_query for the PDBe MCP Servers MCP server. Add the server to your MCP client (Claude Desktop, Cursor, Windsurf and others), then check which tools your installed version makes available. Tool availability can depend on configuration and credentials. A server handshake does not verify this tool’s behavior. See the full listing for setup details.
Install PDBe MCP Servers
uvx pdbe-mcp-serverOther tools in PDBe MCP Servers (14)
Structure determination method
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.
Bound ligands
Type of molecule (protein, DNA, RNA, etc.)
Source organism
PDB entry identifier
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.
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.
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.
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.
Structure release date
Structure resolution (Å)
Execute Solr-style search queries with flexible field selection, filter queries, facets, grouping, sorting, and pagination options.
Structure title/description