Unofficial DB MCP Server

Model Context Protocol (MCP) server providing access to the comprehensive DB pharmaceutical database (17,430+ drugs).

Features

• Single unified tool with 16 methods
• High-performance SQLite backend: <10ms queries, ~50-100MB memory usage
• Access to 17,430 drug records (13,166 small molecules + 4,264 biotech)
• Comprehensive pharmaceutical data including:
  • Drug names, descriptions, classifications
  • Clinical indications and mechanisms of action
  • Chemical structures (SMILES, InChI)
  • Drug interactions and contraindications
  • Target proteins, enzymes, carriers, transporters
  • Metabolic pathways
  • Market products and regulatory information
  • Pharmacokinetics (half-life search) and toxicity data
  • Salt forms and external database identifiers
  • Drug similarity search

Installation

# Clone and install dependencies
cd drugbank-mcp-server
npm install

Obtain the DB database:

1. Download the full database ZIP from your DB account
2. Extract the XML and place it at data/full database.xml

# Build the SQLite database and copy source files
npm run build

Usage

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

Tool

Single unified tool with multiple methods accessed via the method parameter.

Methods

1. search_by_name

Search drugs by name (supports partial matching).

Note: DB uses chemical names as primary identifiers. Search for “Acetylsalicylic” to find aspirin, “Ibuprofen” not “Advil”, etc.

{
  "method": "search_by_name",
  "query": "Acetylsalicylic",
  "limit": 20
}

2. get_drug_details

Get complete drug information by DB ID.

{
  "method": "get_drug_details",
  "drugbank_id": "EXPT00475"
}

Returns full drug record including:

• All identifiers (DB ID, CAS, UNII)
• Clinical information (indication, mechanism, toxicity)
• Pharmacokinetics (absorption, metabolism, half-life)
• Chemical properties
• Interactions (drug-drug, food)
• Targets and enzymes

3. search_by_indication

Find drugs by medical indication.

{
  "method": "search_by_indication",
  "query": "pain",
  "limit": 20
}

4. search_by_target

Find drugs by target protein/enzyme.

{
  "method": "search_by_target",
  "target": "COX-2",
  "limit": 20
}

5. get_drug_interactions

Get all drug-drug interactions for a specific drug.

{
  "method": "get_drug_interactions",
  "drugbank_id": "DB00945"
}

6. search_by_atc_code

Search by ATC (Anatomical Therapeutic Chemical) classification code.

{
  "method": "search_by_atc_code",
  "code": "N02BA",
  "limit": 20
}

7. get_pathways

Get metabolic pathways for a drug.

{
  "method": "get_pathways",
  "drugbank_id": "DB00945"
}

8. search_by_structure

Search by chemical structure (SMILES or InChI).

{