一个模型上下文协议（MCP）服务器，提供访问蛋白质数据库（PDB）——全球关于蛋白质、核酸和复杂组装体三维结构信息的存储库。

特色

工具

• search_structures：通过关键词、蛋白名称或PDB编号搜索PDB数据库中的蛋白质结构
• get_structure_info：获取特定PDB结构的详细信息
• download_structure：多种格式（PDB、mmCIF、mmTF、XML）下载结构坐标
• search_by_uniprot：查找与UniProt登录关联的PDB结构
• get_structure_quality：获取结构质量指标和验证数据

资源

• pdb://structure/{pdb_id}：PDB ID的完整结构信息
• pdb://coordinates/{pdb_id}：结构坐标（PDB格式）
• pdb://mmcif/{pdb_id}：mmCIF格式的结构数据
• pdb://validation/{pdb_id}：结构验证数据与质量指标
• pdb://ligands/{pdb_id}：配体和结合位点信息
• pdb://search/{query}：查找匹配查询的结构

安装

用途

使用Claude桌面

PDB MCP Server

A Model Context Protocol (MCP) server that provides access to the Protein Data Bank (PDB) - the worldwide repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies.

Features

Tools

• search_structures: Search PDB database for protein structures by keyword, protein name, or PDB ID
• get_structure_info: Get detailed information for a specific PDB structure
• download_structure: Download structure coordinates in various formats (PDB, mmCIF, mmTF, XML)
• search_by_uniprot: Find PDB structures associated with a UniProt accession
• get_structure_quality: Get structure quality metrics and validation data

Resources

• pdb://structure/{pdb_id}: Complete structure information for a PDB ID
• pdb://coordinates/{pdb_id}: Structure coordinates in PDB format
• pdb://mmcif/{pdb_id}: Structure data in mmCIF format
• pdb://validation/{pdb_id}: Structure validation data and quality metrics
• pdb://ligands/{pdb_id}: Ligand and binding site information
• pdb://search/{query}: Search results for structures matching the query

Installation

npm install
npm run build

Usage

With Claude Desktop

Add to your claude_desktop_config.json:

{
  "mcpServers": {
    "pdb-server": {
      "command": "node",
      "args": ["/path/to/pdb-server/build/index.js"]
    }
  }
}

Example Queries

1. Search for insulin structures:

   Use the search_structures tool to find insulin protein structures
   

2. Get information about a specific structure:

   Get detailed information about PDB structure 1ABC using get_structure_info
   

3. Download structure coordinates:

   Download the PDB file for structure 1ABC using download_structure
   

4. Find structures for a UniProt protein:

   Find PDB structures for UniProt accession P01308 using search_by_uniprot
   

5. Check structure quality:

   Get validation metrics for PDB structure 1ABC using get_structure_quality
   

6. Access resources directly:

   Show me the resource pdb://structure/1abc
   

API Integration

This server integrates with:

• RCSB PDB REST API (https://data.rcsb.org/): For structure metadata and information
• RCSB PDB Search API (https://search.rcsb.org/): For advanced search capabilities
• RCSB PDB File Download (https://files.rcsb.org/): For structure file downloads

Structure Data Formats

• PDB: Original Protein Data Bank format
• mmCIF: Macromolecular Crystallographic Information File (newer standard)
• mmTF: Macromolecular Transmission Format (binary, compressed)
• XML: Extensible Markup Language format

Quality Metrics

The server provides various structure quality indicators:

• Resolution (for X-ray crystallography)
• R-work and R-free values
• Ramachandran plot statistics