// SCAN REPORT

AlphaFold Sovereign MCP

54 tools. 4 can modify or destroy data without limits.

4 write tools that can modify data. Rate limits recommended.

Last updated: 29 Jun 2026

4 can modify or destroy data

50 read-only

54 tools total

Community server · catalogue entry verified 29/06/2026

How to control AlphaFold Sovereign MCP ↓

TOOL MAP

What AlphaFold Sovereign MCP exposes to your agents

Read (50) Write / Execute (4) Destructive / Financial (0)

Running more than one server? Check your whole stack →

MOST DANGEROUS TOOLS

High Risk

The most dangerous AlphaFold Sovereign MCP tools

Write · Medium export_protein_set export_protein_set Write · Medium export_research_dataset export_research_dataset Write · Medium generate_variant_clinical_report generate_variant_clinical_report Write · Medium resolve_icd10_to_mondo resolve_icd10_to_mondo

4 of AlphaFold Sovereign MCP's 54 tools can modify, destroy, or commit something on every call — and an agent calls them with no built-in limits.

POLICY

How to control AlphaFold Sovereign MCP

PolicyLayer is an MCP gateway — it sits between your AI agents and AlphaFold Sovereign MCP, and nothing reaches the server without passing your rules. These are the rules we recommend:

Rate limit write operations

{
  "export_protein_set": {
    "limits": [
      {
        "counter": "export_protein_set_per_hour",
        "window": "hour",
        "max": 30,
        "scope": "grant"
      }
    ]
  }
}

Prevents bulk unintended modifications from agents caught in loops.

Cap read operations

{
  "analyze_structural_confidence": {
    "limits": [
      {
        "counter": "analyze_structural_confidence_per_minute",
        "window": "minute",
        "max": 60,
        "scope": "grant"
      }
    ]
  }
}

Controls API costs and prevents retry loops from exhausting upstream rate limits.

Create a free account and register AlphaFold Sovereign MCP — nothing to install.
Add these rules — paste them, or build them visually. Tune the limits to your setup.
Point your MCP client (Claude, Cursor, anything) at your gateway URL.

ENFORCE POLICY ON ALPHAFOLD SOVEREIGN →

Instant setup, no code required.

FULL CATALOGUE

All 54 AlphaFold Sovereign MCP tools

WRITE 4 tools

Write export_protein_set export_protein_set Write export_research_dataset export_research_dataset Write generate_variant_clinical_report generate_variant_clinical_report Write resolve_icd10_to_mondo resolve_icd10_to_mondo

READ 50 tools

Read analyze_structural_confidence analyze_structural_confidence Read assess_target_druggability assess_target_druggability Read batch_go_lookup batch_go_lookup Read batch_protein_analysis batch_protein_analysis Read batch_structures batch_structures Read check_availability check_availability Read classify_variant_acmg classify_variant_acmg Read compare_disease_target_overlap compare_disease_target_overlap Read compare_protein_topology compare_protein_topology Read compare_proteins_topologically compare_proteins_topologically Read compute_information_content Compute Information Content (IC) for GO terms using corpus frequencies. Read compute_semantic_similarity compute_semantic_similarity Read compute_topology_fingerprint compute_topology_fingerprint Read detect_domains detect_domains Read detect_intrinsically_disordered detect_intrinsically_disordered Read extract_pae_matrix extract_pae_matrix Read filter_by_organism filter_by_organism Read find_drug_gene_network find_drug_gene_network Read find_drug_repurposing_candidates find_drug_repurposing_candidates Read find_evolutionary_structural_shifts find_evolutionary_structural_shifts Read find_similar_proteins find_similar_proteins Read get_advanced_topology get_advanced_topology Read get_cache_statistics Get statistics about the local structure cache. Read get_common_disease_targets get_common_disease_targets Read get_disease_targets get_disease_targets Read get_domain_annotations get_domain_annotations Read get_enriched_protein get_enriched_protein Read get_features get_features Read get_gene_phenotype_profile get_gene_phenotype_profile Read get_go_hierarchy get_go_hierarchy Read get_knowledge_graph_stats Return statistics about the local knowledge graph. Read get_orphan_disease_atlas get_orphan_disease_atlas Read get_plddt_profile Get detailed per-residue pLDDT confidence profile. Read get_protein_families get_protein_families Read get_structure get_structure Read get_target_diseases get_target_diseases Read get_topology get_topology Read lookup_disease lookup_disease Read lookup_phenotype lookup_phenotype Read map_disease_drug_landscape map_disease_drug_landscape Read phenotype_to_structures phenotype_to_structures Read predict_disorder Predict intrinsically disordered regions (IDRs) from pLDDT scores. Read query_protein_database query_protein_database Read query_variant_database query_variant_database Read score_binding_pocket_geometry score_binding_pocket_geometry Read search_by_go_term search_by_go_term Read search_diseases search_diseases Read search_structures search_structures Read synthesize_protein_dossier synthesize_protein_dossier Read triage_variant_3d triage_variant_3d

FAQ

Questions about AlphaFold Sovereign MCP

How do I prevent bulk modifications through AlphaFold Sovereign MCP? +

The AlphaFold Sovereign MCP server has 4 write tools including export_protein_set, export_research_dataset, generate_variant_clinical_report. Set a rate limit in your policy -- for example, 10 calls per hour prevents an agent from making more than 10 modifications per hour. PolicyLayer enforces this at the gateway, before calls reach AlphaFold Sovereign MCP.

How many tools does the AlphaFold Sovereign MCP server expose? +

54 tools across 2 categories: Read, Write. 50 are read-only. 4 can modify, create, or delete data.

How do I enforce a policy on AlphaFold Sovereign MCP? +

Register the AlphaFold Sovereign MCP server in PolicyLayer, apply the suggested rules above (adjust the limits to your use case), and point your AI client at the PolicyLayer proxy URL instead of the server directly. Your agents keep the same tools; PolicyLayer evaluates every call against policy before it executes. Nothing to install, live in minutes.

Enforce policy on every AlphaFold Sovereign MCP tool call.

Deterministic rules across all 54 AlphaFold Sovereign MCP tools. Per-identity grants. Full audit log. Live in minutes. Nothing to install.

ENFORCE POLICY ON ALPHAFOLD SOVEREIGN →

Instant setup, no code required.

54 AlphaFold Sovereign MCP tools catalogued and risk-classified — across an index of 43,000+ MCP servers.