pdb_id

MCP tool from PDBe MCP Servers by PDBeurope

PDB entry identifier

How to use it

pdb_id is exposed by the PDBe MCP Servers MCP server. Add the server to your MCP client (Claude Desktop, Cursor, Windsurf and others), and the pdb_id tool becomes available to the model automatically. See the full listing for setup details and every tool this server provides.

Install PDBe MCP Servers

$uvx pdbe-mcp-server

FULL PDBE MCP SERVERS LISTING

Other tools in PDBe MCP Servers (31)

cypher_query

(required): The Cypher query to execute. Only MATCH and OPTIONAL MATCH queries are allowed.

experimental_method

Structure determination method

facet

(optional): Enable Solr faceting

facet_fields

(optional): Field facet string or array, sent as facet.field

facet_limit

, facetmincount, facetsort (optional): Common facet controls

facet_queries

(optional): Query facet string or array, sent as facet.query

filters

(optional): Backwards-compatible alias for fl

(optional): Field list as a string or array of field names to include in results

(optional): Filter query string or array of filter query strings

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.

group

(optional): Enable Solr grouping

group_field

(optional): Grouping field string or array, sent as group.field

group_limit

, groupoffset, groupsort (optional): Common grouping controls

ligand_name

Bound ligands

molecule_type

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

node_labels

(required): List of exact, case-sensitive node labels to verify.

organism_scientific_name

Source organism

params

(optional): Object of additional Solr parameters for advanced use

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.

query

(required): Raw Solr query string passed as q (e.g., :, pdbid:1cbs, text:kinase, resolution:[0 TO 2.0])

release_date

Structure release date

resolution

Structure resolution (Å)

rows

(optional): Number of results to return (default: 10)

run_pdbe_search_query

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

sort

(optional): Sort criteria (e.g., releasedate desc, resolution asc)