score_binding_pocket_geometry

MCP tool from Alphafold Sovereign MCP by smaniches

Geometric pocket detection + heuristic druggability index

How to use it

Project documentation lists score_binding_pocket_geometry for the Alphafold Sovereign MCP MCP server. Add the server to your MCP client (Claude Desktop, Cursor, Windsurf and others), then check which tools your installed version makes available. Tool availability can depend on configuration and credentials. A server handshake does not verify this tool’s behavior. See the full listing for setup details.

Install Alphafold Sovereign MCP

$alphafold-sovereign-mcp
FULL ALPHAFOLD SOVEREIGN MCP LISTING

Other tools in Alphafold Sovereign MCP (29)

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

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)