smaniches/alphafold-sovereign-mcp

Overview

A Model Context Protocol server for biomedical data, providing access to AlphaFold DB and eight public sources. It includes a SQLite knowledge graph and supports offline mode. The tool explicitly limits clinical use.

Best for

Best for
Researchers and developers building biomedical MCP tools

Use cases

• Query protein structures from AlphaFold DB
• Integrate biomedical data into MCP clients
• Run offline biomedical searches with a local knowledge graph

How to use

Install

uvx alphafold-sovereign-mcp

Tools exposed

• lookup_disease
• search_diseases
• lookup_phenotype
• get_gene_phenotype_profile
• get_disease_targets
• get_target_diseases
• get_common_disease_targets
• triage_variant_3d
• phenotype_to_structures
• get_orphan_disease_atlas
• compare_disease_target_overlap
• resolve_icd10_to_mondo
• generate_variant_clinical_report
• assess_target_druggability
• synthesize_protein_dossier
• map_disease_drug_landscape
• classify_variant_acmg
• find_drug_repurposing_candidates
• analyze_structural_confidence
• compute_topology_fingerprint

Tested with

Claude Desktop

Notes

A Model Context Protocol server for biomedical data, providing access to AlphaFold DB and eight public sources. It includes a SQLite knowledge graph and supports offline mode. The tool explicitly limits clinical use.

4 stars on GitHub. Last updated 2026-09-03. Licensed Apache-2.0.

Use cases

• Query protein structures from AlphaFold DB
• Integrate biomedical data into MCP clients
• Run offline biomedical searches with a local knowledge graph

Pros

• Offline mode enables local use without network dependency
• SQLite knowledge graph supports structured queries
• Open source with a Python implementation

Cons

• Limited to AlphaFold DB and eight public sources
• Explicitly not intended for clinical use
• Requires MCP environment setup for integration

Indexed from awesome-mcp-servers-punkpeye and enriched against its public facts.