PDBe MCP Servers

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by PDBeurope

PDBe MCP Servers integrate Protein Data Bank Europe resources with LLMs via Model Context Protocol. Provides seamless access to protein structure data through API tools and graph database schema assistance for intelligent Cypher query generation, bridging structural biology and AI research.

Install

$uvx pdbe-mcp-server

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Tools (32)

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

fl

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

fq

(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

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.

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)

start

(optional): Starting index for pagination (default: 0)

title

Structure title/description