openpharma-org/pubchem-mcp

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)

Usage

Add the server to your MCP client configuration:

{
  "mcpServers": {
    "pubchem-mcp-server": {
      "command": "node",
      "args": ["/path/to/pubchem-mcp-server/build/index.js"],
      "env": {}
    }
  }
}

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

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"
  }
}

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

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
  }
}