How do I connect Alphafold Sovereign MCP Server to Claude?

The listing records `alphafold-sovereign-mcp` as its setup step. Run it, then follow the repository's instructions for the client configuration; the listing names Claude Desktop as compatible clients.

Is Alphafold Sovereign MCP Server free?

The listed licence is Apache-2.0. Check the upstream terms for permitted use and commercial requirements; a public repository does not by itself mean the software is free or open source. Connected APIs and hosted services may have separate charges.

What can Alphafold Sovereign MCP Server do?

Alphafold Sovereign MCP Server documents 30 tools to the agent, including analyze_structural_confidence, assess_target_druggability, classify_variant_acmg. The descriptions above come from project documentation. A live handshake does not test individual tool behavior.

Alphafold Sovereign MCP

Unclaimed

by smaniches

BioMed MCP over AlphaFold DB + 8 public sources, with SQLite knowledge graph, offline mode, and explicit clinical-use limits.

Install

$alphafold-sovereign-mcp

Set up this server

Compare servers My Stack

This server needs project-specific setup. Follow the project instructions; no reusable public launch command is available yet.

Project instructions

alphafoldbioinformaticsclaudeclinvardrug-discoveryknowledge-graphmcpmcp-servermodel-context-protocolprotein-structure

Is this your MCP server?

This listing was auto-indexed from the public record. Claim it to edit the page, set compatibility and unlock growth tools. Takes under two minutes.

Claim this server

Security profile

Claimed and verified servers get a weekly static scan that shows what the code can reach: external services, environment variables, shell commands, agent configuration folders, plus any dependencies with known advisories. Claim this listing to get one. How the security profile works

30 of 30 tools

Documented tools (30)

From project documentation. A server handshake does not verify each tool’s description or behavior.

analyze_structural_confidence

mean pLDDT + confidence tier + PAE-derived domain boundaries

assess_target_druggability

UniProt → HOT/WARM/COLD/NOTDRUGGABLE tier

classify_variant_acmg

HGVS → ACMG/AMP criteria checklist (PVS1, PM2, PP3, BP4, BP7, BS1, PP5)

compare_disease_target_overlap

Jaccard similarity of target sets for two diseases

compare_proteins_topologically

Pairwise L2 fingerprint-distance matrix for 2–10 proteins

compute_topology_fingerprint

64-dim TDA fingerprint (Betti numbers β₀ β₁ β₂)

detect_intrinsically_disordered

IDR map (linkers, tails, long IDRs)

export_research_dataset

Export tables to JSON for pandas/ML pipelines

find_drug_gene_network

Traverse the local drug–gene–disease graph

find_drug_repurposing_candidates

MONDO → candidates ranked by OT evidence × ChEMBL phase

find_evolutionary_structural_shifts

Cross-species structural divergence (TDA + Ensembl orthologs)

generate_variant_clinical_report

HGVS → multi-source report + draft ACMG/AMP criteria

get_common_disease_targets

Parallel profiling across curated MONDO diseases

get_disease_targets

Top drug targets for a MONDO disease (Open Targets)

get_gene_phenotype_profile

HPO phenotypes + gnomAD constraint for a gene

get_knowledge_graph_stats

Database size, entity counts, last activity

get_orphan_disease_atlas

Orphanet → MONDO → HPO + OT targets

get_protein_structure

Retrieve an AlphaFold model: metadata, download URLs, optional coordinates

get_target_diseases

Top diseases for a UniProt target (Open Targets)

lookup_disease

MONDO record + hierarchy + ICD cross-references

lookup_phenotype

HPO term + associated diseases

map_disease_drug_landscape

MONDO → approved drugs + pipeline + ChEMBL phase counts

phenotype_to_structures

HPO → diseases → OT targets → UniProt IDs

query_protein_database

Search locally stored protein assessments

query_variant_database

Search locally stored variant triage results

resolve_icd10_to_mondo

ICD-10 code → MONDO disease record

score_binding_pocket_geometry

Geometric pocket detection + heuristic druggability index

search_diseases

Full-text MONDO ontology search

synthesize_protein_dossier

UniProt → multi-source briefing

triage_variant_3d

HGVS → ClinVar + gnomAD constraint (disease/structure context: pointer notes)

Tool change history

Compared across complete checks of the same configuration. Tools were listed, not invoked. Input-schema changes are not measured here.

No complete tool checks yet.

FAQ

Questions about Alphafold Sovereign MCP Server

How do I connect Alphafold Sovereign MCP Server to Claude?: The listing records `alphafold-sovereign-mcp` as its setup step. Run it, then follow the repository's instructions for the client configuration; the listing names Claude Desktop as compatible clients.
Is Alphafold Sovereign MCP Server free?: The listed licence is Apache-2.0. Check the upstream terms for permitted use and commercial requirements; a public repository does not by itself mean the software is free or open source. Connected APIs and hosted services may have separate charges.
What can Alphafold Sovereign MCP Server do?: Alphafold Sovereign MCP Server documents 30 tools to the agent, including analyze_structural_confidence, assess_target_druggability, classify_variant_acmg. The descriptions above come from project documentation. A live handshake does not test individual tool behavior.