AlphaFold-MCP-Server

概述

AlphaFold MCP 服务器提供了广泛的蛋白质结构分析工具，包括多种格式的结构检索（PDB、CIF、BCIF、JSON）、置信度分析、批量处理功能，以及与 PyMOL 和 ChimeraX 等可视化工具的集成。它使研究人员能够高效访问和分析 AlphaFold 的庞大蛋白质结构预测集合。服务器实现了适当的错误处理和速率限制，以确保与 AlphaFold API 的稳定交互。

试试问 AI

装完之后，这里有 5 个你可以让 AI 做的事：

• get_structureuniprotId (required), format (optional)

  Retrieve AlphaFold structure prediction for a specific UniProt ID

  试试:Get the structure for protein P04637 in JSON format试试:Fetch AlphaFold prediction for Q8N726 in PDB format
• download_structureuniprotId (required), format (optional)

  Download AlphaFold structure file in specified format

  试试:Download PDB file for protein P04637试试:Get BCIF format structure for Q8N726
• check_availabilityuniprotId (required)

  Check if AlphaFold structure prediction is available for a UniProt ID

  试试:Check if structure exists for P04637试试:Verify availability for protein Q8N726
• search_structuresquery (required), organism (optional), size (optional)

  Search for available AlphaFold structures by protein name or gene

  试试:Search for structures related to p53 protein试试:Find all structures from Homo sapiens
• get_confidence_scoresuniprotId (required), threshold (optional)

  Get per-residue confidence scores for a structure prediction

  试试:Get confidence scores for protein P04637试试:Show residues with confidence above 80 for Q8N726
• batch_structure_infouniprotIds (required), format (optional)

  Get structure information for multiple proteins simultaneously

  试试:Get info for proteins P04637, P53350, and P63151试试:Retrieve summary data for multiple UniProt IDs
• compare_structuresuniprotIds (required)

  Compare multiple AlphaFold structures for analysis

  试试:Compare structures of P04637, P53350, and P63151试试:Analyze differences between proteins P12345 and P23456
• export_for_pymoluniprotId (required), includeConfidence (optional)

  Export structure data formatted for PyMOL visualization

  试试:Export P04637 structure for PyMOL with confidence coloring试试:Prepare P53350 for visualization in PyMOL
• list_by_organismorganism (required), size (optional)

  List all available structures for a specific organism

  试试:List all structures from Escherichia coli试试:Get available human protein structures
• get_organism_statsorganism (required)

  Get statistics about AlphaFold coverage for an organism

  试试:Get coverage statistics for Homo sapiens试试:Show AlphaFold stats for Arabidopsis thaliana
• find_similar_structuresuniprotId (required), organism (optional)

  Find AlphaFold structures similar to a given protein

  试试:Find structures similar to P04637试试:Show proteins with similar structure to Q8N726 from E. coli
• get_prediction_metadatauniprotId (required)

  Get metadata about the prediction including version, date, and quality metrics

  试试:Get metadata for protein P04637 prediction试试:Show quality metrics for Q8N726

可对比工具

安装

# 克隆或创建服务器目录
npm install

# 构建服务器
npm run build

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

FAQ

支持哪些文件格式的结构下载？

服务器支持 PDB、CIF、BCIF 和 JSON 格式的结构检索和下载。

如何处理大型批量请求？

服务器自动分块处理大请求，并包含内置延迟以防止 API 过载，同时处理批量操作。

AlphaFold-MCP-Server 对比