🧬 GWAS-MCP: Bioinformatics MCP Server

A powerful Model Context Protocol (MCP) server for GWAS and bioinformatics research. Seamlessly integrates with Claude Desktop and other MCP clients to provide AI-powered access to major biological databases.

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✨ Features

🔬 Protein & Gene Lookup

• UniProt - Search proteins by name, gene, or ID
• Ensembl - Gene information and variant details
• NCBI Gene - Comprehensive gene database

🧪 Clinical & Variants

• ClinVar - Clinical variant interpretations (pathogenic/benign)
• GWAS Catalog - Genome-wide association studies
• GTEx - Expression quantitative trait loci (eQTL)

🔗 Protein Interactions & Networks

• STRING - Protein-protein interactions
• InterPro - Protein domains and families

🏗️ Structures & Pathways

• AlphaFold - AI-predicted protein structures
• PDB - Experimental 3D structures
• KEGG - Metabolic and signaling pathways

💊 Drug Discovery

• Open Targets - Drug target validation & disease associations
• PharmGKB - Pharmacogenomics & drug-gene interactions

🏥 Genetic Diseases

• OMIM - Online Mendelian Inheritance in Man

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🚀 Quick Start

Installation

pip install gwas-mcp

Claude Desktop Configuration

Add to your claude_desktop_config.json:

{
  "mcpServers": {
    "gwas-bioinformatics": {
      "command": "python",
      "args": ["-m", "gwas_mcp.server"]
    }
  }
}

Config file location:

• Windows: %APPDATA%\Claude\claude_desktop_config.json
• macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
• Linux: ~/.config/Claude/claude_desktop_config.json

Restart Claude Desktop

After adding the configuration, restart Claude Desktop to load the MCP server.

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🛠️ Available Tools

Protein & Gene Tools

Tool	Description
search_uniprot	Search UniProt by protein name, gene, or ID
get_protein_details	Get detailed protein info (function, domains, GO terms)
search_ncbi_gene	Search NCBI Gene database
search_ensembl_gene	Get gene location and details from Ensembl
get_variant_info	Get SNP/variant info by rsID
get_interpro_domains	Get protein domain information

Clinical & Variant Tools

Tool	Description
search_clinvar	Search ClinVar for clinical variants
get_clinvar_variant	Get clinical interpretation for a variant
annotate_snps	Annotate SNPs with functional consequences
query_gwas_catalog	Query GWAS Catalog for associations
get_eqtl_data	Get eQTL data from GTEx

Protein Interaction Tools

Tool	Description
get_protein_interactions	Find interacting proteins (STRING)
get_interaction_network	Get network between multiple proteins
get_functional_enrichment	Pathway/GO enrichment analysis

Structure & Pathway Tools

Tool	Description
get_alphafold_structure	Get AI-predicted structure
search_alphafold	Search AlphaFold database
search_pdb_structures	Search PDB for 3D structures
get_pdb_structure	Get PDB structure details
search_kegg_pathway	Search KEGG pathways
get_kegg_pathway	Get pathway genes and details
get_gene_pathways	Find pathways for a gen

... View full README on GitHub