Unofficial PubChem MCP Server

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

Features

🔍 Chemical Search & Retrieval (6 tools)

search_compounds - Search by name, CAS number, formula, or identifier
get_compound_info - Detailed compound information by CID
search_by_smiles - Exact SMILES string matching
search_by_inchi - InChI/InChI key search
search_by_cas_number - CAS Registry Number lookup
get_compound_synonyms - All names and synonyms

🧬 Structure Analysis & Similarity (5 tools)

search_similar_compounds - Tanimoto similarity search
substructure_search - Find compounds containing substructures
superstructure_search - Find larger compounds containing query
get_3d_conformers - 3D structural information
analyze_stereochemistry - Chirality and isomer analysis

⚗️ Chemical Properties & Descriptors (6 tools)

get_compound_properties - Molecular weight, logP, TPSA, etc.
calculate_descriptors - Comprehensive molecular descriptors
predict_admet_properties - ADMET predictions
assess_drug_likeness - Lipinski Rule of Five analysis
analyze_molecular_complexity - Synthetic accessibility
get_pharmacophore_features - Pharmacophore mapping

🧪 Bioassay & Activity Data (5 tools)

search_bioassays - Find biological assays
get_assay_info - Detailed assay protocols
get_compound_bioactivities - All activity data for compounds
search_by_target - Find compounds tested against targets
compare_activity_profiles - Cross-compound comparisons

⚠️ Safety & Toxicity (4 tools)

get_safety_data - GHS hazard classifications
get_toxicity_info - LD50, carcinogenicity data
assess_environmental_fate - Biodegradation analysis
get_regulatory_info - FDA, EPA regulations

🔗 Cross-References & Integration (4 tools)

get_external_references - Links to ChEMBL, DrugBank, etc.
search_patents - Chemical patent information
get_literature_references - PubMed citations
batch_compound_lookup - Bulk processing (up to 200 compounds)

Resource Templates

Access PubChem data through URI patterns:

pubchem://compound/{cid} - Complete compound data
pubchem://structure/{cid} - 2D/3D structure information
pubchem://properties/{cid} - Molecular properties
pubchem://bioassay/{aid} - Bioassay data
pubchem://similarity/{smiles} - Similarity search results
pubchem://safety/{cid} - Safety and toxicity data

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

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" } }

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 } }

Architecture

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:

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

PubChem MCP Server