A Model Context Protocol (MCP) server for accessing PDBe (Protein Data Bank in Europe) structural biology data and services
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# PDBe MCP Servers 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. 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](https://github.com/astral-sh/uv)** - Fast Python package manager and dependency resolver ## Installation ### Quick Start **Run directly from PyPI:** ```bash 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: 1. **Clone and navigate to the repository:** ```bash git clone https://github.com/PDBeurope/PDBe-MCP-Servers.git cd PDBe-MCP-Servers ``` 2. **Create a virtual environment:** ```bash uv venv ``` 3. **Install with uv:** ```bash uv pip install . ``` ## AI Client Integration ### Configuration 1. **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. 2. **Add the recommended PDBe MCP server configuration.** For JS…
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