run_pdbe_search_query

MCP tool from PDBe MCP Servers by PDBeurope

Execute Solr-style search queries with flexible field selection, filter queries, facets, grouping, sorting, and pagination options.

How to use it

Project documentation lists run_pdbe_search_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-server
FULL PDBE MCP SERVERS LISTING

Other tools in PDBe MCP Servers (14)

experimental_method

Structure determination method

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.

ligand_name

Bound ligands

molecule_type

Type of molecule (protein, DNA, RNA, etc.)

organism_scientific_name

Source organism

pdb_id

PDB entry identifier

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_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_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_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_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.

release_date

Structure release date

resolution

Structure resolution (Å)

title

Structure title/description