Used for making HTTP requests to the PubChem API, enabling reliable data retrieval from the PubChem chemical database.
Used for package management and running server operations like installation, building, and starting the PubChem MCP server.
Provides access to literature references for chemical compounds, allowing users to retrieve PubMed citations related to specific chemicals in the PubChem database.
Provides type safety for all API inputs and comprehensive validation for PubChem data operations.
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 datapubchem://structure/{cid}
- 2D/3D structure informationpubchem://properties/{cid}
- Molecular propertiespubchem://bioassay/{aid}
- Bioassay datapubchem://similarity/{smiles}
- Similarity search resultspubchem://safety/{cid}
- Safety and toxicity data
Installation
Usage
Basic Compound Search
Structure Analysis
Bioactivity Analysis
Safety Information
Batch Processing
Integration with Other MCP Servers
This PubChem server integrates perfectly with other chemical/biological databases:
Complete Chemical Informatics Pipeline
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
Chemical Similarity Analysis
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:
remote-capable server
The server can be hosted and run remotely because it primarily relies on remote services or has no dependency on the local environment.
Tools
Provides access to over 110 million chemical compounds with tools for chemical search, structure analysis, property calculation, bioassay data retrieval, and safety information through the PubChem database.
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