How do I connect PDBe MCP Servers MCP Server to Claude?

Run `claude mcp add pdbe-mcp-servers -- uvx pdbe-mcp-server` in Claude Code, or add the same command and arguments under mcpServers in Cursor's mcp.json or Claude Desktop's claude_desktop_config.json, then restart the client. The blocks above are ready to paste.

Is PDBe MCP Servers MCP Server free?

The listed licence is Apache-2.0. Check the upstream terms for permitted use and commercial requirements; a public repository does not by itself mean the software is free or open source. Connected APIs and hosted services may have separate charges.

What can PDBe MCP Servers MCP Server do?

PDBe MCP Servers MCP Server documents 15 tools to the agent, including experimental_method, get_pdbe_search_schema, ligand_name. The descriptions above come from project documentation. A live handshake does not test individual tool behavior.

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.

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01 / Choose your client

02 / Before you connect

Authentication is not specified. Check the project instructions before connecting.

Install the runtime required by the project and make it available to your client.

Project instructionsEnvironment variable names (optional)

Use names from the project instructions, separated by commas. Enter names only, never secret values.

03 / Add the configuration

Source: generated from public install instructions

claude mcp add --transport stdio 'pdbe-mcp-servers' -- 'uvx' 'pdbe-mcp-server'

Run in your terminal after replacing any placeholders.

04 / Check it in your client

Open your client’s MCP settings and confirm the server connects and lists its tools. A copied configuration does not confirm a working connection.

ai-integrationapi-serverbioinformaticsknowledge-graphllm-toolsmcppdbeprotein-structurespythonstructural-biology

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15 of 15 tools

Documented tools (15)

From project documentation. A server handshake does not verify each tool’s description or behavior.

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)

run_pdbe_search_query

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

title

Structure title/description

Tool change history

Compared across complete checks of the same configuration. Tools were listed, not invoked. Input-schema changes are not measured here.

No complete tool checks yet.

FAQ

Questions about PDBe MCP Servers MCP Server

How do I connect PDBe MCP Servers MCP Server to Claude?: Run `claude mcp add pdbe-mcp-servers -- uvx pdbe-mcp-server` in Claude Code, or add the same command and arguments under mcpServers in Cursor's mcp.json or Claude Desktop's claude_desktop_config.json, then restart the client. The blocks above are ready to paste.
Is PDBe MCP Servers MCP Server free?: The listed licence is Apache-2.0. Check the upstream terms for permitted use and commercial requirements; a public repository does not by itself mean the software is free or open source. Connected APIs and hosted services may have separate charges.
What can PDBe MCP Servers MCP Server do?: PDBe MCP Servers MCP Server documents 15 tools to the agent, including experimental_method, get_pdbe_search_schema, ligand_name. The descriptions above come from project documentation. A live handshake does not test individual tool behavior.