AlphaFold Sovereign MCP
Integrates AlphaFold DB and eight other biomedical data sources into MCP tools for variant clinical reporting, disease-target analysis, structural intelligence, and drug repurposing, with results persisted to a local SQLite knowledge graph.
Caution. Specific findings reduced this grade. They are listed on the page. Grades reflect the full trust pyramid: code, verification depth, and reputation. New projects cap at C until adoption is earned.
How we verified
Verified is a snapshot. Live keeps it current, and builds your track record.
⚡ Connect GitHub → continuous verification on every pushwhy connect →Who stands behind it
smaniches
Source: Glama
Claim it to get a verified publisher badge, a free copy of our full audit findings, and direct contact for any high-priority issues we find. Or connect your repo for our deepest verification, Live Monitored: read-only, revoke anytime. What we access →
Install from
The grade above is for the source repository. Registries can serve a different version, so we mark the ones we were not able to read.
These names and descriptions are the publisher's own, read from the source code. We print them as written. Our assessment is the findings above, not this list.
get_structureRetrieve an AlphaFold protein structure by UniProt ID. PROPRIETARY TOOL - TOPOLOGICA LLC Operation (Cache-First Sovereign Strategy): 1. Check local cache (dynamically indexed, grows with usage) 2. If not found, fetch from AlphaFold DB online 3. Auto-cache fetched structures for future sovereign acce…
search_structuresSearch local AlphaFold structure cache. PROPRIETARY TOOL - TOPOLOGICA LLC Searches the sovereign cache (dynamically indexed) by UniProt ID pattern. Includes both pre-downloaded structures and previously-fetched online structures. Args: pattern: Glob-style pattern (e.g., 'A0A*', 'P123*') limit: Maxim…
batch_structuresRetrieve multiple AlphaFold structures in batch. PROPRIETARY TOOL - TOPOLOGICA LLC Efficiently retrieves multiple structures with optional features. Args: uniprot_ids: List of UniProt IDs (max 50) include_features: Compute structural features for each Returns: Batch results with structure details
get_featuresCompute detailed structural features for a protein. PROPRIETARY TOOL - TOPOLOGICA LLC Available features: - secondary_structure: Alpha-helix, beta-strand, coil classification - binding_pockets: Cavity detection with druggability scoring - confidence: pLDDT-based quality assessment - contacts: Local …
get_topologyCompute topological features (persistent homology) for a protein. PROPRIETARY TOOL - TOPOLOGICA LLC Mathematical Foundation: Vietoris-Rips filtration on C-alpha atom point cloud. Computes: - beta_0: Connected components (protein domains) - beta_1: Loops/tunnels (structural motifs) - beta_2: Voids/ca…
check_availabilityCheck availability of structures (local cache and online). PROPRIETARY TOOL - TOPOLOGICA LLC Checks both local cache (instant) and AlphaFold DB (network). Args: uniprot_ids: List of UniProt IDs to check Returns: Availability status for each ID
get_cache_statisticsGet statistics about the local structure cache. PROPRIETARY TOOL - TOPOLOGICA LLC Returns information about: - Number of local structures - Cache directories and mode - Storage locations - Configuration status
get_enriched_proteinGet comprehensive protein information combining AlphaFold structure + UniProt metadata. PROPRIETARY TOOL - TOPOLOGICA LLC This tool provides UNIQUE VALUE by combining: 1. AlphaFold structural data (3D coordinates, pLDDT confidence) 2. UniProt functional annotations (function, GO terms, active sites)…
batch_go_lookupGet GO terms for hundreds of proteins at once. PROPRIETARY TOOL - TOPOLOGICA LLC Efficiently fetches GO annotations for large protein sets. Uses local cache when available, fetches from UniProt when needed. Results are persisted for future sovereign access. Use Cases: - Training data extraction for …
search_by_go_termFind all proteins with a specific GO annotation. PROPRIETARY TOOL - TOPOLOGICA LLC Searches the inverted index for proteins annotated with a GO term. Essential for building training sets for function prediction. Use Cases: - Find all kinases (GO:0016301) - Find all membrane proteins (GO:0016020) - B…
get_go_hierarchyNavigate GO term parent/child relationships. PROPRIETARY TOOL - TOPOLOGICA LLC Fetches GO term hierarchy from QuickGO API. Essential for GO term propagation in function prediction. Use Cases: - Understand term specificity - Propagate annotations up the hierarchy - Find related terms for training Arg…
export_protein_setExport filtered proteins to TSV/CSV for ML pipelines. PROPRIETARY TOOL - TOPOLOGICA LLC Creates tabular exports suitable for: - Training machine learning models - Data analysis in pandas/R - Integration with CAFA pipelines Args: uniprot_ids: List of proteins to export output_format: 'tsv' or 'csv' i…
find_similar_proteinsFind proteins similar by sequence or structure. PROPRIETARY TOOL - TOPOLOGICA LLC Uses k-mer based sequence similarity for fast approximate matching. For structure similarity, uses C-alpha RMSD when structures available. Args: uniprot_id: Query protein similarity_type: 'sequence' or 'structure' thre…
get_domain_annotationsRetrieve Pfam/InterPro domain annotations. PROPRIETARY TOOL - TOPOLOGICA LLC Fetches domain annotations from UniProt cross-references. Domains are key features for function prediction. Args: uniprot_ids: List of proteins sources: Annotation sources (Pfam, InterPro, etc.) Returns: Domain annotations …
filter_by_organismFilter proteins by organism from local cache. PROPRIETARY TOOL - TOPOLOGICA LLC Searches local AlphaFold structures for organism-specific proteins. Essential for species-specific function prediction. Args: organism: Organism name or taxonomy ID limit: Maximum results include_go_summary: Include GO t…
get_protein_familiesCluster proteins by sequence or GO term similarity. PROPRIETARY TOOL - TOPOLOGICA LLC Groups proteins into families based on similarity. Useful for identifying functionally related proteins. Args: uniprot_ids: Proteins to cluster clustering_method: 'sequence' or 'go_terms' similarity_threshold: Clus…
extract_pae_matrixExtract Predicted Aligned Error (PAE) matrix from AlphaFold structure. PROPRIETARY TOOL - TOPOLOGICA LLC PAE measures predicted distance error between residue pairs. Low PAE (<5Å) indicates high confidence in relative positioning. Returns: PAE matrix with statistics (min, max, mean, domain blocks)
detect_domainsDetect protein domains from PAE matrix clustering. PROPRIETARY TOOL - TOPOLOGICA LLC Uses PAE values to identify independently folded domains. Low intra-domain PAE + high inter-domain PAE = domain boundary. Returns: List of domains with residue ranges, confidence, and contacts
predict_disorderPredict intrinsically disordered regions (IDRs) from pLDDT scores. PROPRIETARY TOOL - TOPOLOGICA LLC Low pLDDT (<50) often indicates disorder/flexibility. Returns IDR regions, propensity profile, and disorder statistics.
get_plddt_profileGet detailed per-residue pLDDT confidence profile. PROPRIETARY TOOL - TOPOLOGICA LLC pLDDT categories: - Very high (>90): High confidence - High (70-90): Good confidence - Low (50-70): Caution - Very low (<50): Likely disordered
compute_information_contentCompute Information Content (IC) for GO terms using corpus frequencies. PROPRIETARY TOOL - TOPOLOGICA LLC IC(t) = -log(P(t)) where P(t) = freq(t)/max_freq Higher IC = more specific term = more informative Supports batch computation for efficiency.
compute_semantic_similarityCompute semantic similarity between GO terms. PROPRIETARY TOOL - TOPOLOGICA LLC Methods: - Resnik: IC of Most Informative Common Ancestor (MICA) - Lin: 2*IC(MICA) / (IC(t1) + IC(t2)) - Jiang: 1 - (IC(t1) + IC(t2) - 2*IC(MICA)) - Wang: Graph-based with semantic contribution Returns pairwise similarit…
get_advanced_topologyCompute advanced topological features with full TDA pipeline. PROPRIETARY TOOL - TOPOLOGICA LLC Features: - Persistence diagrams (birth-death pairs) - Betti curves over filtration - Persistence landscapes - Persistence images (vectorization) - Euler characteristic curve Mathematical Foundation: Viet…
compare_protein_topologyCompare topological features between two proteins. PROPRIETARY TOOL - TOPOLOGICA LLC Distance Metrics: - Wasserstein (Earth Mover's): Optimal transport between diagrams - Bottleneck: Max matching distance - Landscape L2: Euclidean distance in landscape space Lower distance = more similar topology.
batch_protein_analysisComprehensive batch analysis of multiple proteins with progress tracking. PROPRIETARY TOOL - TOPOLOGICA LLC Runs selected analyses on all proteins: - Structure retrieval - Feature extraction - Topology computation - Disorder prediction - Domain detection Returns aggregated results with statistics.
lookup_diseaseRetrieve a disease record from the MONDO unified disease ontology.
search_diseasesSearch for diseases by name or keyword using the MONDO ontology.
lookup_phenotypeRetrieve an HPO phenotype term with associated disease annotations.
get_gene_phenotype_profileReturn all HPO phenotypes associated with a gene, plus gnomAD constraint.
get_disease_targetsReturn top protein targets for a disease with Open Targets evidence scores.
get_target_diseasesReturn all diseases associated with a protein target via Open Targets.
get_common_disease_targetsProfile the top drug targets for a curated set of common diseases in one call.
triage_variant_3dComprehensive clinical triage for a missense variant.
phenotype_to_structuresMap a clinical phenotype to the protein structures of its disease targets.
get_orphan_disease_atlasMap an Orphanet rare disease to its MONDO record, HPO phenotypes, and protein targets.
compare_disease_target_overlapCompare the protein target landscapes of two diseases.
resolve_icd10_to_mondoResolve an ICD-10 clinical code to MONDO disease ontology terms.
query_variant_databaseSearch the local knowledge graph for stored variants.
query_protein_databaseRecall proteins already stored in the local knowledge graph.
get_knowledge_graph_statsReturn statistics about the local knowledge graph.
export_research_datasetExport the stored knowledge-graph data for downstream analysis.
find_drug_gene_networkTraverse the local knowledge graph from a seed entity.
generate_variant_clinical_reportGenerate a multi-source variant interpretation report.
assess_target_druggabilityComprehensive druggability assessment for a protein target.
synthesize_protein_dossierGenerate a complete protein intelligence dossier from 7 data sources.
map_disease_drug_landscapeMap the complete therapeutic landscape for a disease.
classify_variant_acmgGenerate a draft ACMG/AMP variant classification framework.
find_drug_repurposing_candidatesRank existing clinical-stage drugs as repurposing candidates for a disease.
analyze_structural_confidenceAnalyze AlphaFold structural confidence using pLDDT and PAE.
compute_topology_fingerprintCompute a rotation-invariant topological fingerprint of a protein's fold.
compare_proteins_topologicallyCompare multiple proteins using a TDA-fingerprint distance.
find_evolutionary_structural_shiftsQuantify cross-species structural and sequence divergence for a gene.
score_binding_pocket_geometryIdentify and score putative binding pockets from AlphaFold geometry.
detect_intrinsically_disorderedMap intrinsically disordered regions (IDRs) using pLDDT as proxy.
get_protein_structureRetrieve a protein's AlphaFold model: metadata, download URLs, optional coordinates.
ALPHAFOLD_OFFLINEDisGeNET, needs its own free API key); set =1 to refuseALPHAFOLD_ALLOW_HOSTSALPHAFOLD_RATE_LIMITNCBI_API_KEYDISGENET_API_KEYAFSMCP_DISABLE_KG_SEEDrelationships; disable with =1) and can beALPHAFOLD_KG_PATHTool annotations
30/55 tools have annotations
Add readOnlyHint or destructiveHint annotations to every tool so hosts can warn users before invoking.
All four hints declared on every tool
55/55 tools missing one or more hints — get_structure (missing: readOnlyHint, destructiveHint, idempotentHint, openWorldHint); search_structures (missing: readOnlyHint, destructiveHint, idempotentHint, openWorldHint); batch_structures (missing: readOnlyHint, destructiveHint, idempotentHint, openWorldHint), +52 more. OpenAI's directory rejects tools where any of the four hints are missing or non-boolean.
For every tool, set all four hints (readOnlyHint, destructiveHint, idempotentHint, openWorldHint) to explicit true/false values that match the handler’s actual behaviour.
Descriptions match behaviour
1 tool describes read intent but its handler mutates — export_protein_set (line 4689: with open(export_path, 'w', encoding='utf-8', newline='\n') as f:)
Rename the tool, rewrite the description, or move the side-effect into a separate clearly-named tool.
Tool inputs are validated
53/55 tool handlers declare input schemas (96%)
Declare an inputSchema with zod/joi/yup on every tool definition.
Tool handlers catch errors
43/55 tool handlers wrap calls in try/catch (78%)
Wrap each tool handler body in try/catch and return a structured error response.
Tests exist
No test files found
Add tests that exercise each declared tool.
Tool description accuracy
export_protein_set: description implies read-only but handler writes/deletes/executes
Update tool descriptions to accurately reflect all capabilities — especially write, delete, or execute operations.
Claim the listing to review these findings one by one and send us a correction where you disagree, straight to the team. Claiming also means we tell you when the grade moves, and reach you first if we find anything urgent.
[](https://m8ven.ai/mcp/smaniches/alphafold-sovereign-mcp)?variant=verified from the URL.Vetting this one by hand? Tool Check is an MCP that scores other MCPs. Add it once and ask Claude, ChatGPT, or any MCP client to grade a server, surface CVEs, check the publisher, and suggest safer alternatives — before you install.
https://m8ven.ai/api/mcp/tool-check