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Retrieves and analyzes PDB, AlphaFold, GPCRdb, SAbDab, ProteinsPlus, and BindingDB data for druggability assessment, binding-site characterization, and structural-confidence scoring. Run Python computations for enrichment and statistics.
How this skill is triggered — by the user, by Claude, or both
Slash command
/tooluniverse:tooluniverse-structural-proteomicsThe summary Claude sees in its skill listing — used to decide when to auto-load this skill
Comprehensive structural data integration using ToolUniverse tools across PDB, AlphaFold, GPCRdb, SAbDab, and proteomics databases for drug target validation.
Comprehensive structural data integration using ToolUniverse tools across PDB, AlphaFold, GPCRdb, SAbDab, and proteomics databases for drug target validation.
PDBeSIFTS_get_best_structures and RCSBGraphQL_get_structure_summaryalphafold_get_summaryPDBe_get_structure_ligands and BindingDB_get_ligands_by_uniprotProteinsPlus_predict_binding_sitesWhen analysis requires computation (statistics, data processing, scoring, enrichment), write and run Python code via Bash. Don't describe what you would do — execute it and report actual results. Use ToolUniverse tools to retrieve data, then Python (pandas, scipy, statsmodels, matplotlib) to analyze it.
Resolution determines valid conclusions: <2A = atom positions visible; 2-3A = side chains reliable, drug design supported; >3A = backbone only, binding site unreliable. Do not over-interpret low-resolution structures.
RCSBAdvSearch_search_structures (query_type, query_value, rows), RCSBData_get_entry (entry_id), RCSBGraphQL_get_structure_summary (pdb_id), RCSBGraphQL_get_ligand_info (pdb_id), RCSB_get_chemical_component (comp_id)
pdbe_get_entry_summary (pdb_id), PDBe_get_structure_ligands (pdb_id), PDBe_get_bound_molecules (pdb_id), PDBeSearch_search_structures (query, rows), PDBeSIFTS_get_best_structures (uniprot_id), PDBeSIFTS_get_all_structures (uniprot_id), PDBe_KB_get_ligand_sites (pdb_id), PDBe_KB_get_interface_residues (pdb_id), PDBeValidation_get_quality_scores (pdb_id)
PDBePISA_get_interfaces (pdb_id), PDBePISA_get_assemblies (pdb_id)
alphafold_get_prediction (qualifier=UniProt), alphafold_get_summary (qualifier), alphafold_get_annotations (qualifier)
ProteinsPlus_predict_binding_sites (pdb_id, chain), BindingDB_get_ligands_by_uniprot (uniprot_id), BindingDB_get_ligands_by_pdb (pdb_id), BindingDB_get_targets_by_compound (smiles)
Foldseek_search_structure (sequence, mode="tmalign"), Foldseek_get_result (ticket)
GPCRdb_get_protein (protein), GPCRdb_get_structures (protein), GPCRdb_get_ligands (protein), GPCRdb_get_mutations (protein). Accepts entry names, gene symbols (auto-converted to {symbol.lower()}_human), or UniProt accessions.
SAbDab_search_structures (query/antigen), SAbDab_get_structure (pdb_id), TheraSAbDab_search_therapeutics (query), TheraSAbDab_search_by_target (target)
InterPro_get_protein_domains (uniprot_id), Pfam_get_protein_annotations (uniprot_id), UniProt_get_entry_by_accession (accession)
ProteomeXchange_search_datasets (query), ProteomeXchange_get_dataset (dataset_id)
Phase 0: Resolve protein → UniProt ID, gene symbol, organism
Phase 1: PDBeSIFTS_get_best_structures → RCSBGraphQL_get_structure_summary → PDBeValidation
Phase 2: alphafold_get_prediction/summary → compare pLDDT with experimental coverage
Phase 3: IF GPCR → GPCRdb; IF antibody target → SAbDab/TheraSAbDab
Phase 4: InterPro/Pfam domain mapping → identify unresolved regions
Phase 5: Summary table (PDB ID, method, resolution, ligands, coverage, quality)
Decisions: Resolution <2.5A for drug design. X-ray > Cryo-EM > NMR > AlphaFold for binding sites. Holo > apo structures.
Phase 1: PDBe_get_structure_ligands + RCSBGraphQL_get_ligand_info + PDBe_KB_get_ligand_sites
Phase 2: ProteinsPlus_predict_binding_sites → druggability score, pocket residues
Phase 3: BindingDB_get_ligands_by_pdb/uniprot → Ki, Kd, IC50
Phase 4: RCSB_get_chemical_component for key ligands
Filter artifacts: GOL, EDO, SO4, PEG, ACT, CL, NA. Keep cofactors (ATP, NAD, HEM) and catalytic metals (ZN, MG) if relevant.
Phase 1: Find co-crystal structures → filter for drug/analogs
Phase 2: BindingDB affinity data (Ki, Kd, IC50)
Phase 3: ProteinsPlus + PDBe-KB binding site characterization
Phase 4: PDBeValidation quality → binding site well-resolved?
Phase 5: AlphaFold + Foldseek structural comparison
Phase 6: GPCR-specific (if applicable) → active/inactive states, pharmacology, resistance mutations
Phase 7: Antibody-specific (if applicable) → epitope mapping
Phase 8: Evidence integration
| Tool | Mistake | Correct |
|---|---|---|
alphafold_get_prediction/summary | uniprot_id | qualifier |
GPCRdb_get_protein | gene_name | protein |
PDBeSIFTS_get_best_structures | gene symbol | uniprot_id (e.g., "P04637") |
Foldseek_search_structure | mode="3diaa" | mode="tmalign" |
SAbDab_search_structures | name | query or antigen |
RCSB_get_chemical_component | ligand_id | comp_id |
| Tier | Confidence |
|---|---|
| T1 | Co-crystal (<2.5A) + binding affinity data |
| T2 | Experimental structure + computational prediction |
| T3 | AlphaFold + pocket analysis + known ligand analogs |
| T4 | Homology model or low-resolution only |
| Metric | High | Acceptable | Caution |
|---|---|---|---|
| Resolution | <2.0A (X-ray) / <3.0A (cryo-EM) | 2.0-2.5A / 3.0-4.0A | >3.0A / >4.5A |
| R-free | <0.25 | 0.25-0.30 | >0.30 |
| AlphaFold pLDDT | >90 | 70-90 | <70 (disordered) |
DoGSiteScorer >0.6 = druggable; <0.4 = unlikely druggable. PISA assemblies should be cross-validated with SEC-MALS/native MS.
operation is internal, not a public parameternpx claudepluginhub mims-harvard/tooluniverse --plugin tooluniverseRetrieves protein structures from RCSB PDB, PDBe, and AlphaFold with disambiguation, quality assessment (resolution, R-factor, pLDDT), and metadata. Useful for structure-quality comparison and selecting structures for drug design or modeling.
Accesses AlphaFold DB's 200M+ predicted protein structures by UniProt ID using BioPython or REST API. Downloads PDB/mmCIF files, analyzes pLDDT/PAE confidence, bulk-fetches proteomes via Google Cloud.
Retrieves AlphaFold-predicted protein structures by UniProt ID, downloads PDB/mmCIF files, and analyzes confidence metrics (pLDDT, PAE) for drug discovery and structural biology.