DGIdb MCP Server

Preprint: https://www.biorxiv.org/content/10.64898/2026.01.18.700012v1

This is a Cloudflare Workers-based Model Context Protocol (MCP) server that provides tools for querying the DGIdb (Drug Gene Interaction Database) API.

DGIdb streamlines the search for druggable therapeutic targets through the aggregation, categorization, and curation of drug and gene data from publications and expert resources.

Example of DGIdb MCP Server on Claude Desktop

User Prompt:

"What genes interact with the drug Ibrutinib and by what mechanism of interaction according to DGIdb?"

Tool Called: get_gene_interactions_for_drug_list

Request

{
  "drugNames": "Ibrutinib"
}

API Response

{
  "Instructions": "Interaction Score: Scoring metric based on the evidence supporting an interaction.
                  Interaction Direction: Describes the effect of the interaction on the biological activity of the gene.
                  Interaction Type:  Nature of the association between a particular drug and gene.
                  When returning information to users you MUST cite URLs used for specific information."

  "API Results": [
    { "gene": "PLCG2",
      "interactionScore": 4.61,
      "interactionTypes": [],
      "sources": ["CGI", "DoCM"],
      "pmidUrls": ["https://pubmed.ncbi.nlm.nih.gov/24869598/"]},

    { "gene": "MYD88",
      "interactionScore": 1.0,
      "interactionTypes": [],
      "sources": ["CIViC", "PharmGKB", "CGI", "DoCM"],
      "pmidUrls": []
    },
    { "gene": "BTK",
      "interactionScore": 0.38,
      "interactionTypes": [
          {
            "type": "inhibitor",
            "directionality": "INHIBITORY"
          }
      ],
      "sources": ["CIViC", "PharmGKB", "CGI", "DoCM", "TTD", "MyCancerGenome", "TdgClinicalTrial", "ChEMBL", "COSMIC"],
      "pmidUrls": [
          "https://pubmed.ncbi.nlm.nih.gov/25222877/",
          "https://pubmed.ncbi.nlm.nih.gov/24869598/",
          "https://pubmed.ncbi.nlm.nih.gov/27199251/"
        ]
    },
    ...
  ]
}

Claude Response

According to DGIdb, Ibrutinib interacts with multiple genes. Here are the top interactions ranked by interaction score:

Primary Target

Gene	Interaction Type	Direction	Score	Sources
BTK	Inhibitor	Inhibitory	0.38	CGI, CIViC, PharmGKB, ChEMBL, and others

BTK (Bruton's Tyrosine Kinase) is the primary therapeutic target of ibrutinib. The drug acts as an irreversible inhibitor, blocking BTK's enzymatic activity. Supporting publications: PMID: 25222877, PMID: 24869598, PMID: 27199251

Resistance/Response Biomarkers

Gene	Score	Sources
PLCG2	4.61	CGI, DoCM — PMID: 24869598
MYD88	1.54	CGI, CIViC, PharmGKB

PLCG2 and MYD88 are associated with ibrutinib resistance or response prediction rather than being direct drug targets.

Additional Inhibitory Targets

Gene	Interaction Type	Score	Source
ENUR2	Inhibitor	0.31	Guide to Pharmacology
BMX	Not specified	0.26	TTD
EFNA1	Inhibitor	0.14	Guide to Pharmacology
EPS15	Inhibitor	0.13	Guide to Pharmacology
TEC	Inhibitor	0.11	Guide to Pharmacology
EPHA8	Inhibitor	0.11	Guide to Pharmacology

Ibrutinib is known to have off-target kinase inhibition beyond BTK, which may contribute to both efficacy and side effects.

View the original chat here: https://claude.ai/share/8e9224cd-4927-4337-9a76-cc4ab8f95d93

Configuring Claude Desktop

Example video taken from CIViC MCP

MCP.Claude.Setup.1.480p.mp4

Install Node.js (https://nodejs.org/)

Click "LTS" (Recommended for Most Users) — this gives you Node.js and npx Download and install it like any normal app

Once installed: On Windows: Open “Command Prompt” or “PowerShell” On macOS: Open “Terminal”

Then run:

node -v
npx -v

Confirm that both give versions.

Accessing DGIdb via MCP

Add this configuration to your claude_desktop_config.json file:

{
  "mcpServers": {
    "lars-dgidb-mcp-server": {
    "command": "npx",
    "args": [
          "mcp-remote",
          "https://dgidb-mcp-server.larscivic.workers.dev/mcp"
        ]
    }
  }
}

Joint Access to DGIdb and CIViC via MCP

Add this configuration to your claude_desktop_config.json file:

{
"mcpServers": {
    "lars-civic-mcp-server": {
    "command": "npx",
    "args": [
          "mcp-remote",
          "https://civic-mcp-server-v2.larscivic.workers.dev/mcp"
        ]
      },

    "lars-dgidb-mcp-server": {
    "command": "npx",
    "args": [
          "mcp-remote",
          "https://dgidb-mcp-server.larscivic.workers.dev/mcp"
        ]
      }
  }
}

Usage

Once configured, restart Claude Desktop. The server provides 4 main tools:

1. get_drug_info: Gets drug info including approval, if used in immunotherapy, and other drug attributes for a list of drugs.
2. get_gene_info: Gets gene category info for a list of genes.
3. get_drug_interactions_for_gene_list: Gets drugs that interact with a list of genes.
4. get_gene_interactions_for_drug_list: Gets genes that interact with a list of drugs.