PubChem MCP Server: AI-Powered Molecular Query & Structure Generation

Empowering large language models to seamlessly query molecular databases and generate accurate structure files—bridging AI innovation with chemical discovery.

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About PubChem MCP Server

What is PubChem MCP Server: AI-Powered Molecular Query & Structure Generation?

PubChem MCP Server is an AI-driven Python-based tool enabling programmable access to PubChem's vast chemical compound database. Built on the Model Context Protocol (MCP), it empowers researchers and developers to retrieve molecular data via compound names/CIDs and generate 3D structural models. This server acts as a bridge between computational workflows and PubChem's repository, offering both command-line access and integration with MCP-enabled platforms like Claude AI tools.

How to Use PubChem MCP Server: AI-Powered Molecular Query & Structure Generation?

Command-Line Interface

pubchem-mcp  [--format {JSON/CSV/XYZ}] [--include-3d]

Example: pubchem-mcp aspirin --format XYZ --include-3d retrieves aspirin's 3D coordinates.

MCP Server Setup

Launch server: pubchem-mcp-server
Configure MCP settings file with server details
Restart Claude applications for integration

PubChem MCP Server Features

Key Features of PubChem MCP Server

Multi-format support: JSON, CSV, and XYZ (3D structural) outputs
AI-enhanced queries: Natural language processing capabilities for ambiguous compound name searches
3D modeling: RDKit-powered structural generation for molecular visualization
Platform integration: Native MCP compatibility for AI toolchains
Batch processing: Programmatic access for high-throughput workflows

Use Cases for PubChem MCP Server

Drug discovery pipelines requiring rapid molecular property retrieval
Teaching tools for visualizing chemical structures in 3D
Automated chemical database curation workflows
AI model training with standardized PubChem data formats
Regulatory compliance checks via programmatic CAS number verification

PubChem MCP Server FAQ

FAQ: PubChem MCP Server

Do I need RDKit?

RDKit is optional but recommended for advanced 3D structure generation. Install via RDKit.

What formats are supported?

Primary formats: JSON (metadata), CSV (tabular data), XYZ (3D coordinates). Extended formats available via API.

Why use MCP integration?

Enables seamless connectivity with AI platforms like Claude, allowing context-aware molecular queries through natural language prompts.

Is this free to use?

Yes, MIT-licensed open-source tool. Commercial use permitted with proper attribution.

Content

PubChem MCP Server (Python版本)

这是一个用Python实现的Model Context Protocol (MCP)服务器，提供PubChem化合物数据检索功能。

功能

通过化合物名称或PubChem CID检索化合物数据
支持多种输出格式：JSON、CSV和XYZ
支持3D结构数据检索（XYZ格式）
提供命令行接口和MCP服务器接口

安装

基本安装

# 从源代码安装
git clone https://github.com/yourusername/pubchem-mcp-server.git
cd pubchem-mcp-server/python_version
pip install .

# 或者直接从PyPI安装（如果已发布）
pip install pubchem-mcp-server

安装RDKit支持（可选）

RDKit用于增强3D结构生成功能，但不是必需的：

pip install "pubchem-mcp-server[rdkit]"

或者，您可以单独安装RDKit：

conda install -c conda-forge rdkit
# 或
pip install rdkit

使用方法

命令行接口

# 基本用法
pubchem-mcp aspirin

# 指定输出格式
pubchem-mcp aspirin --format CSV

# 获取3D结构（XYZ格式）
pubchem-mcp aspirin --format XYZ --include-3d

# 查看帮助
pubchem-mcp --help

作为MCP服务器

启动服务器：

pubchem-mcp-server

将服务器添加到MCP配置文件中（通常位于~/.claude-dev/settings/cline_mcp_settings.json或~/Library/Application Support/Claude/claude_desktop_config.json）：

{
  "mcpServers": {
    "pubchem": {
      "command": "python",
      "args": ["-m", "pubchem_mcp_server.server"],
      "env": {},
      "disabled": false,
      "autoApprove": []
    }
  }
}

重启Claude应用程序或Claude开发环境，然后您就可以使用PubChem MCP工具了。

API

主要函数

get_pubchem_data(query, format='JSON', include_3d=False): 获取PubChem化合物数据
get_xyz_structure(cid, smiles, compound_info): 获取化合物的XYZ格式3D结构

依赖项

Python >= 3.8
requests >= 2.25.0
MCP SDK（可选，用于MCP服务器功能）
rdkit >= 2022.9.1（可选，用于增强3D结构生成功能）

关于MCP SDK

MCP SDK是Model Context Protocol的软件开发工具包，用于创建MCP服务器。由于MCP SDK可能不在PyPI上公开可用，您可能需要手动安装它。如果您只想使用命令行接口来检索PubChem数据，则不需要安装MCP SDK。

许可证

MIT

致谢

PubChem数据由美国国家生物技术信息中心(NCBI)提供
基于原始TypeScript版本的PubChem MCP服务器重新实现

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