Is PDBe MCP Servers safe to use?

PDBe MCP Servers has no known CVEs as of the latest MCPpedia security scan. It does not require authentication, so any local process can connect — keep this in mind in shared environments. Licensed under Apache-2.0.

How do I install PDBe MCP Servers?

PDBe MCP Servers supports copy-paste install configs on its MCPpedia page for Claude Desktop, Cursor, and Claude Code. Scroll to the Quick Install section and select your client.

What can PDBe MCP Servers do?

PDBe MCP Servers provides 2 tools: get_pdbe_search_schema, run_pdbe_search_query. See the full tools list on the server page for descriptions and parameters.

What AI clients work with PDBe MCP Servers?

PDBe MCP Servers is compatible with claude-desktop, cursor, claude-code. It uses stdio and sse and http transport.

Is PDBe MCP Servers actively maintained?

PDBe MCP Servers is actively maintained — last commit was 4 days ago. It has 36 GitHub stars.

PDBe MCP Servers

Name: PDBe MCP Servers
Author: PDBeurope

pdbe-mcp-server · 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.

36 2 tools GitHub PyPI

No known CVEs

Apache-2.0 license

Actively maintained

Last commit 4d ago

Works with most clients

Transport: stdio, sse, http

2 tools · ~563 tok

Grade B · 0.3% of 200K ctx

Edit this pageView history

Data AI / ML

Step 1

Install in your client

Config is the same across clients — only the file and path differ.

Supported in Claude Desktopstdio, sse, http · Node 18+

Paste into ~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "PDBe API Server": {
      "args": [
        "pdbe-mcp-server",
        "--server-type",
        "pdbe_api_server"
      ],
      "command": "uvx"
    },
    "PDBe Search Server": {
      "args": [
        "pdbe-mcp-server",
        "--server-type",
        "pdbe_search_server"
      ],
      "command": "uvx"
    }
  }
}

Are you the author?

Add this badge to your README to show your security score and help users find safe servers.

Embed in your READMEAbout badges →

[![MCPpedia Score](https://mcppedia.org/api/badge/pdbe-mcp-servers)](https://mcppedia.org/s/pdbe-mcp-servers)

Read me

What PDBe MCP Servers does

A set of Model Context Protocol (MCP) servers that provides seamless access to the Protein Data Bank in Europe (PDBe) API and PDBe Search. These servers expose PDBe's comprehensive structural biology data as MCP tools, enabling direct integration with any AI client that supports MCP.

Test This Server

Run this in your terminal to verify the server starts. Then let us know if it worked — your result helps other developers.

uvx 'pdbe-mcp-server' 2>&1 | head -1 && echo "✓ Server started successfully"

After testing, let us know if it worked:

Loading README…

Scored, not listed

Why this score

Five weighted categories — click any category to see the underlying evidence.

Score breakdown

84/100across 5 weighted dimensions

How we score →

0255075100

−16

Security

Maintenance

Efficiency

Documentation

Compatibility

Categoriesclick a row to see evidence

Security

OSV.dev

No known CVEs.

Checked pdbe-mcp-server against OSV.dev.

Inventory

Tools (2)

Click any tool to inspect its schema.

~563 tokens total

Community

Reviews

Be the first to review

Have you used this server?

Share your experience — it helps other developers decide.

How easy was setup?Did it work reliably?How was the documentation?

Frequently Asked Questions

Is PDBe MCP Servers safe to use?: PDBe MCP Servers has no known CVEs as of the latest MCPpedia security scan. It does not require authentication, so any local process can connect — keep this in mind in shared environments. Licensed under Apache-2.0.
How do I install PDBe MCP Servers?: PDBe MCP Servers supports copy-paste install configs on its MCPpedia page for Claude Desktop, Cursor, and Claude Code. Scroll to the Quick Install section and select your client.
What can PDBe MCP Servers do?: PDBe MCP Servers provides 2 tools: get_pdbe_search_schema, run_pdbe_search_query. See the full tools list on the server page for descriptions and parameters.
What AI clients work with PDBe MCP Servers?: PDBe MCP Servers is compatible with claude-desktop, cursor, claude-code. It uses stdio and sse and http transport.
Is PDBe MCP Servers actively maintained?: PDBe MCP Servers is actively maintained — last commit was 4 days ago. It has 36 GitHub stars.

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Community

Discussion

Start a conversation

Ask a question, share a tip, or report an issue.

Has anyone used this with Cursor?How do you handle auth?Any alternatives?

Edit this pageView history

Data AI / ML

Step 1

Install in your client

Config is the same across clients — only the file and path differ.

Supported in Claude Desktopstdio, sse, http · Node 18+

Paste into ~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "PDBe API Server": {
      "args": [
        "pdbe-mcp-server",
        "--server-type",
        "pdbe_api_server"
      ],
      "command": "uvx"
    },
    "PDBe Search Server": {
      "args": [
        "pdbe-mcp-server",
        "--server-type",
        "pdbe_search_server"
      ],
      "command": "uvx"
    }
  }
}

Are you the author?

Add this badge to your README to show your security score and help users find safe servers.

Embed in your READMEAbout badges →

[![MCPpedia Score](https://mcppedia.org/api/badge/pdbe-mcp-servers)](https://mcppedia.org/s/pdbe-mcp-servers)

Read me

What PDBe MCP Servers does

Test This Server

Run this in your terminal to verify the server starts. Then let us know if it worked — your result helps other developers.

uvx 'pdbe-mcp-server' 2>&1 | head -1 && echo "✓ Server started successfully"

After testing, let us know if it worked:

README

PDBe MCP Servers

The package also includes an advanced PDBe Graph server for users who run their own local PDBe-KB Neo4j graph database. PDBe does not provide a public running graph database instance for this MCP server to query, so most users should start with the API and Search servers.

Features:

PDBe API Server: Access core structural data through REST API endpoints
PDBe Search Server: Perform advanced Solr-based searches across structural data
PDBe Graph Server: Inspect the graph schema and, with a local PDBe-KB Neo4j setup, query complex relationships and molecular interactions

Prerequisites

Python 3.10+ - Required for the server runtime
uv - Fast Python package manager and dependency resolver

Installation

Quick Start

Run directly from PyPI:

uvx pdbe-mcp-server

The tool is available on PyPI and can be run directly with uvx without any installation step.

Alternative: Local Development Installation

For development work or customization:

Clone and navigate to the repository:

git clone https://github.com/PDBeurope/PDBe-MCP-Servers.git
cd PDBe-MCP-Servers

Create a virtual environment:
```
uv venv
```
Install with uv:
```
uv pip install .
```

AI Client Integration

Configuration

Open your AI client's MCP configuration.

MCP-compatible clients use different settings locations and file formats. Many JSON-based clients use an mcpServers object, while some clients provide commands or a settings UI for adding servers.

Add the recommended PDBe MCP server configuration.

For JSON-based clients that support mcpServers, add:

For PyPI installation (recommended):

{
  "mcpServers": {
    "PDBe API Server": {
      "command": "uvx",
      "args": [
        "pdbe-mcp-server",
        "--server-type",
        "pdbe_api_server"
      ]
    },
    "PDBe Search Server": {
      "command": "uvx",
      "args": [
        "pdbe-mcp-server",
        "--server-type",
        "pdbe_search_server"
      ]
    }
  }
}

For local development installation:

{
  "mcpServers": {
    "PDBe API": {
      "command": "/usr/local/bin/uv",
      "args": [
        "run",
        "--directory",
        "/path/to/your/PDBe-MCP-Servers",
        "pdbe-mcp-server",
        "--server-type",
        "pdbe_api_server"
      ]
    },
    "PDBe Search": {
      "command": "/usr/local/bin/uv",
      "args": [
        "run",
        "--directory",
        "/path/to/your/PDBe-MCP-Servers",
        "pdbe-mcp-server",
        "--server-type",
        "pdbe_search_server"
      ]
    }
  }
}

Note:

For the PyPI installation method, ensure uvx is available in your PATH (this comes with uv)

For local development, ensure that uv is installed and the /path/to/your/PDBe-MCP-Servers matches your actual directory

Add the graph server only if you have a local PDBe-KB Neo4j graph database configured. See Advanced Graph Server Configuration.

Restart or reload your AI client to load the new configuration.

Antigravity Example

In Antigravity, open Manage MCP Servers and select View raw config, or edit ~/.gemini/antigravity/mcp_config.json, then add the PDBe server entries:

{
  "mcpServers": {
    "PDBe API Server": {
      "command": "uvx",
      "args": [
        "pdbe-mcp-server",
        "--server-type",
 

... [View full README on GitHub](https://github.com/PDBeurope/PDBe-MCP-Servers#readme)

Loading README…

Scored, not listed

Why this score

Five weighted categories — click any category to see the underlying evidence.

Score breakdown

84/100across 5 weighted dimensions

How we score →

0255075100

−16

Security

Maintenance

Efficiency

Documentation

Compatibility

Categoriesclick a row to see evidence

Security

OSV.dev

No known CVEs.

Checked pdbe-mcp-server against OSV.dev.

Inventory

Tools (2)

Click any tool to inspect its schema.

~563 tokens total

Community

Reviews

Be the first to review

Have you used this server?

Share your experience — it helps other developers decide.

How easy was setup?Did it work reliably?How was the documentation?

Frequently Asked Questions

Is PDBe MCP Servers safe to use?: PDBe MCP Servers has no known CVEs as of the latest MCPpedia security scan. It does not require authentication, so any local process can connect — keep this in mind in shared environments. Licensed under Apache-2.0.
How do I install PDBe MCP Servers?: PDBe MCP Servers supports copy-paste install configs on its MCPpedia page for Claude Desktop, Cursor, and Claude Code. Scroll to the Quick Install section and select your client.
What can PDBe MCP Servers do?: PDBe MCP Servers provides 2 tools: get_pdbe_search_schema, run_pdbe_search_query. See the full tools list on the server page for descriptions and parameters.
What AI clients work with PDBe MCP Servers?: PDBe MCP Servers is compatible with claude-desktop, cursor, claude-code. It uses stdio and sse and http transport.
Is PDBe MCP Servers actively maintained?: PDBe MCP Servers is actively maintained — last commit was 4 days ago. It has 36 GitHub stars.