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

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... [View full README on GitHub](https://github.com/Augmented-Nature/PubChem-MCP-Server#readme)