Pubchem MCP Server

🚀 Unofficial PubChem MCP Server

A comprehensive Model Context Protocol (MCP) server for accessing the PubChem chemical database. It provides access to over 110 million chemical compounds with extensive molecular properties, bioassay data, and chemical informatics tools.

🚀 Quick Start

This is an unofficial PubChem MCP Server that allows you to access a vast amount of chemical data. You can search for compounds, analyze their structures, and obtain bioassay and safety information.

✨ Features

🔍 Chemical Search & Retrieval (6 tools)

• search_compounds: Search by name, CAS number, formula, or identifier.
• get_compound_info: Get detailed compound information by CID.
• search_by_smiles: Perform exact SMILES string matching.
• search_by_inchi: Conduct InChI/InChI key search.
• search_by_cas_number: Look up by CAS Registry Number.
• get_compound_synonyms: Retrieve all names and synonyms.

🧬 Structure Analysis & Similarity (5 tools)

• search_similar_compounds: Conduct Tanimoto similarity search.
• substructure_search: Find compounds containing substructures.
• superstructure_search: Find larger compounds containing the query.
• get_3d_conformers: Obtain 3D structural information.
• analyze_stereochemistry: Perform chirality and isomer analysis.

⚗️ Chemical Properties & Descriptors (6 tools)

• get_compound_properties: Get molecular weight, logP, TPSA, etc.
• calculate_descriptors: Calculate comprehensive molecular descriptors.
• predict_admet_properties: Make ADMET predictions.
• assess_drug_likeness: Conduct Lipinski Rule of Five analysis.
• analyze_molecular_complexity: Evaluate synthetic accessibility.
• get_pharmacophore_features: Perform pharmacophore mapping.

🧪 Bioassay & Activity Data (5 tools)

• search_bioassays: Find biological assays.
• get_assay_info: Get detailed assay protocols.
• get_compound_bioactivities: Retrieve all activity data for compounds.
• search_by_target: Find compounds tested against targets.
• compare_activity_profiles: Conduct cross - compound comparisons.

⚠️ Safety & Toxicity (4 tools)

• get_safety_data: Get GHS hazard classifications.
• get_toxicity_info: Obtain LD50, carcinogenicity data.
• assess_environmental_fate: Conduct biodegradation analysis.
• get_regulatory_info: Get FDA, EPA regulations.

🔗 Cross - References & Integration (4 tools)

• get_external_references: Get links to ChEMBL, DrugBank, etc.
• search_patents: Obtain chemical patent information.
• get_literature_references: Get PubMed citations.
• batch_compound_lookup: Perform bulk processing (up to 200 compounds).

📦 Installation

# Clone or create the server directory
cd pubchem-server

# Install dependencies
npm install

# Build the server
npm run build

# Run the server
npm start

💻 Usage Examples

🔍 Basic Compound Search

// Search for compounds by name
{
  "tool": "search_compounds",
  "arguments": {
    "query": "aspirin",
    "max_records": 10
  }
}

// Get detailed compound information
{
  "tool": "get_compound_info",
  "arguments": {
    "cid": 2244
  }
}

🧬 Structure Analysis

// Find similar compounds
{
  "tool": "search_similar_compounds",
  "arguments": {
    "smiles": "CC(=O)OC1=CC=CC=C1C(=O)O",
    "threshold": 85,
    "max_records": 50
  }
}

// Analyze molecular properties
{
  "tool": "get_compound_properties",
  "arguments": {
    "cid": 2244,
    "properties": ["MolecularWeight", "XLogP", "TPSA"]
  }
}

🧪 Bioactivity Analysis

// Get bioassay information
{
  "tool": "get_assay_info",
  "arguments": {
    "aid": 1159607
  }
}

// Search compounds by target
{
  "tool": "search_by_target",
  "arguments": {
    "target": "cyclooxygenase",
    "max_records": 100
  }
}

⚠️ Safety Information

// Get safety classifications
{
  "tool": "get_safety_data",
  "arguments": {
    "cid": 2244
  }
}

🔗 Batch Processing

// Process multiple compounds
{
  "tool": "batch_compound_lookup",
  "arguments": {
    "cids": [2244, 5090, 3672],
    "operation": "property"
  }
}

📚 Documentation

🔗 Integration with Other MCP Servers

This PubChem server integrates perfectly with other chemical/biological databases:

🔄 Complete Chemical Informatics Pipeline

1. Target Discovery: UniProt → STRING → AlphaFold
2. Chemical Discovery: PubChem ← → ChEMBL
3. Complete Workflow: Protein → Structure → Interactions → Small Molecules → Bioactivity

🔀 Cross - Database Workflows

• UniProt → PubChem: Find protein targets → Find small molecule ligands.
• PubChem → ChEMBL: Discover compounds → Analyze bioactivity data.
• STRING → PubChem: Protein interactions → Chemical modulators.

⏱️ API Rate Limits

PubChem API guidelines:

• 5 requests per second
• 400 requests per minute maximum
• No API key required
• Respectful usage encouraged

📊 Data Sources

• 110+ million compounds with full chemical data.
• 1.5+ million bioassays with biological activity.
• Chemical properties and computed descriptors.
• 3D conformers and structural data.
• Safety classifications and toxicity information.
• Cross - references to 500+ external databases.

❌ Error Handling

The server includes comprehensive error handling:

• Invalid compound IDs return clear error messages.
• API timeouts are handled gracefully.
• Rate limiting compliance built - in.
• TypeScript validation for all inputs.

🤝 Contributing

This server uses:

• TypeScript for type safety.
• Axios for HTTP requests.
• MCP SDK for protocol compliance.
• PubChem REST API for data access.

📄 License

MIT License - See LICENSE file for details.

🆘 Support

For issues with:

• Server functionality: Check error messages and API responses.
• PubChem API: Refer to official PubChem documentation.
• Chemical data: Validate compound identifiers and search terms.

💡 Examples

💊 Drug Discovery Workflow

// 1. Search for anti-inflammatory compounds
{
  "tool": "search_compounds",
  "arguments": {
    "query": "anti-inflammatory",
    "max_records": 100
  }
}

// 2. Analyze drug-likeness
{
  "tool": "assess_drug_likeness",
  "arguments": {
    "cid": 2244
  }
}

// 3. Check safety profile
{
  "tool": "get_safety_data",
  "arguments": {
    "cid": 2244
  }
}

// 4. Find bioactivity data
{
  "tool": "search_by_target",
  "arguments": {
    "target": "COX-2",
    "activity_type": "IC50"
  }
}

🧪 Chemical Similarity Analysis

// 1. Find similar compounds
{
  "tool": "search_similar_compounds",
  "arguments": {
    "smiles": "your_query_smiles",
    "threshold": 90
  }
}

// 2. Compare molecular properties
{
  "tool": "batch_compound_lookup",
  "arguments": {
    "cids": [1234, 5678, 9012],
    "operation": "property"
  }
}

// 3. Analyze structural features
{
  "tool": "analyze_stereochemistry",
  "arguments": {
    "cid": 1234
  }
}

🔧 Technical Details

The server is built with a modular architecture:

• Type - safe validation for all API inputs.
• Comprehensive error handling with clear messages.
• Efficient batch processing for multiple compounds.
• Resource templates for direct data access.
• Integration - ready for multi - database workflows.

This makes it the most comprehensive chemical informatics MCP server available!

📖 Citation

If you use this project in your research or publications, please cite it as follows:

@misc{pubchemmcp2025, 
author = {Moudather Chelbi},
title = {PubChem MCP Server},
year = {2025},
howpublished = {https://github.com/Augmented-Nature/PubChem-MCP-Server},
note = {Accessed: 2025-06-29}
}