AlphaFold Sovereign MCP
A research-grade biomedical integration that wraps AlphaFold DB and eight other public data sources (MONDO, HPO, Open Targets, ClinVar, gnomAD, DisGeNET, ChEMBL, Ensembl) behind 29 MCP tools. You get variant clinical reports, disease-target landscapes, heuristic druggability scoring, and cross-species structural comparisons via topological data analysis. Everything flows through a local SQLite knowledge graph with query and export capabilities. Ships with 730 tests and 100% coverage, but this is an unfunded independent project with no scientific validation yet and zero certification for clinical or regulated use. Reach for it when you need programmatic access to protein structures and biomedical ontologies in a research context, not production healthcare.
- GitHub stars
- 5
- tools
- 29
- transport
- STDIO
- last updated
- Nov 11, 2026
Tools
29 toolsPublic tool metadata for what this MCP can expose to an agent.
lookup_diseaseMONDO record + hierarchy + ICD cross-references
MONDO record + hierarchy + ICD cross-references
No parameter schema in public metadata yet.
search_diseasesFull-text MONDO ontology search
Full-text MONDO ontology search
No parameter schema in public metadata yet.
lookup_phenotypeHPO term + associated diseases
HPO term + associated diseases
No parameter schema in public metadata yet.
get_gene_phenotype_profileHPO phenotypes + gnomAD constraint for a gene
HPO phenotypes + gnomAD constraint for a gene
No parameter schema in public metadata yet.
get_disease_targetsTop drug targets for a MONDO disease (Open Targets)
Top drug targets for a MONDO disease (Open Targets)
No parameter schema in public metadata yet.
get_target_diseasesTop diseases for a UniProt target (Open Targets)
Top diseases for a UniProt target (Open Targets)
No parameter schema in public metadata yet.
get_common_disease_targetsParallel profiling across curated MONDO diseases
Parallel profiling across curated MONDO diseases
No parameter schema in public metadata yet.
triage_variant_3dHGVS → ClinVar + gnomAD constraint (disease/structure context: pointer notes)
HGVS → ClinVar + gnomAD constraint (disease/structure context: pointer notes)
No parameter schema in public metadata yet.
phenotype_to_structuresHPO → diseases → OT targets → UniProt IDs
HPO → diseases → OT targets → UniProt IDs
No parameter schema in public metadata yet.
compare_disease_target_overlapJaccard similarity of target sets for two diseases
Jaccard similarity of target sets for two diseases
No parameter schema in public metadata yet.
resolve_icd10_to_mondoICD-10 code → MONDO disease record
ICD-10 code → MONDO disease record
No parameter schema in public metadata yet.
generate_variant_clinical_reportHGVS → sourced multi-database report + unreviewed computational signals
HGVS → sourced multi-database report + unreviewed computational signals
No parameter schema in public metadata yet.
assess_target_druggabilityUniProt → uncalibrated HOT/WARM/COLD/NOT_DRUGGABLE heuristic when an observed drug count is available; otherwise explicit tool error
UniProt → uncalibrated HOT/WARM/COLD/NOT_DRUGGABLE heuristic when an observed drug count is available; otherwise explicit tool error
No parameter schema in public metadata yet.
synthesize_protein_dossierUniProt → source-attributed research briefing; errors rather than inventing a druggability tier if source counts are unavailable
UniProt → source-attributed research briefing; errors rather than inventing a druggability tier if source counts are unavailable
No parameter schema in public metadata yet.
map_disease_drug_landscapeMONDO → approved drugs + pipeline + ChEMBL phase counts
MONDO → approved drugs + pipeline + ChEMBL phase counts
No parameter schema in public metadata yet.
classify_variant_acmgHGVS → source evidence + unassessed candidate signals; no automatic clinical class
HGVS → source evidence + unassessed candidate signals; no automatic clinical class
No parameter schema in public metadata yet.
find_drug_repurposing_candidatesMONDO → candidates ranked by OT evidence × ChEMBL phase
MONDO → candidates ranked by OT evidence × ChEMBL phase
No parameter schema in public metadata yet.
analyze_structural_confidencemean pLDDT + confidence tier + PAE-derived domain boundaries
mean pLDDT + confidence tier + PAE-derived domain boundaries
No parameter schema in public metadata yet.
compute_topology_fingerprint64-component exploratory vector; GUDHI computes H₀/H₁ at filtration endpoint; H₂ unavailable
64-component exploratory vector; GUDHI computes H₀/H₁ at filtration endpoint; H₂ unavailable
No parameter schema in public metadata yet.
compare_proteins_topologicallyPairwise L2 fingerprint-distance matrix for 2–10 proteins
Pairwise L2 fingerprint-distance matrix for 2–10 proteins
No parameter schema in public metadata yet.
find_evolutionary_structural_shiftsEnsembl sequence identity + method-labeled structural feature distances; no mixed-scale risk ranking
Ensembl sequence identity + method-labeled structural feature distances; no mixed-scale risk ranking
No parameter schema in public metadata yet.
score_binding_pocket_geometryGeometric pocket detection + heuristic druggability index
Geometric pocket detection + heuristic druggability index
No parameter schema in public metadata yet.
detect_intrinsically_disorderedLow-pLDDT modeled intervals; no validated disorder, linker, or clinical classification
Low-pLDDT modeled intervals; no validated disorder, linker, or clinical classification
No parameter schema in public metadata yet.
get_protein_structureRetrieve an AlphaFold model: metadata, download URLs, optional coordinates
Retrieve an AlphaFold model: metadata, download URLs, optional coordinates
No parameter schema in public metadata yet.
query_variant_databaseSearch locally stored variant triage results
Search locally stored variant triage results
No parameter schema in public metadata yet.
query_protein_databaseSearch locally stored protein assessments
Search locally stored protein assessments
No parameter schema in public metadata yet.
get_knowledge_graph_statsDatabase size, entity counts, last activity
Database size, entity counts, last activity
No parameter schema in public metadata yet.
export_research_datasetExport tables to JSON for pandas/ML pipelines
Export tables to JSON for pandas/ML pipelines
No parameter schema in public metadata yet.
find_drug_gene_networkTraverse the local drug–gene–disease graph
Traverse the local drug–gene–disease graph
No parameter schema in public metadata yet.
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AlphaFold Sovereign MCP
Answering a structural-biology or variant question usually means querying
many public databases by hand — AlphaFold DB, Open Targets, ClinVar,
gnomAD, and more — and reconciling their formats. This server wraps those
sources behind one set of MCP tool calls that run as a local process on
your own machine, with no hosted service of ours in the path, no
telemetry, and a local SQLite knowledge graph that never leaves your disk.
In the default online mode the tools query those public upstreams
directly, so the identifiers you look up are sent to them (and one,
DisGeNET, needs its own free API key); set ALPHAFOLD_OFFLINE=1 to refuse
outbound requests before any socket opens, so no identifier leaves the
machine (the knowledge-graph tools still answer from local data; the
upstream tools report their source as unavailable). "Sovereign" here means
local-first — your compute and stored results stay on your machine — not
that the server runs without a network.
Details
- Repository
- github.com/smaniches/alphafold-sovereign-mcp
- Categories
- Databases, Documents & Knowledge, Data & Analytics
- Package
alphafold-sovereign-mcp- Transport
- STDIO
- Registry
- MCP registry, active
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