Tooluniverse Structural Proteomics

Structural Proteomics for Drug Target Validation

Comprehensive structural data integration using ToolUniverse tools across PDB, AlphaFold, GPCRdb, SAbDab, and proteomics databases for drug target validation.

LOOK UP DON'T GUESS

• PDB structures/resolutions: PDBeSIFTS_get_best_structures and RCSBGraphQL_get_structure_summary
• AlphaFold confidence: alphafold_get_summary
• Ligands/affinities: PDBe_get_structure_ligands and BindingDB_get_ligands_by_uniprot
• Protein-protein binding mutations (ddG): SKEMPI_search_by_structure/SKEMPI_search_by_protein/SKEMPI_get_mutation -- BindingDB's protein-protein equivalent, for interface-mutation affinity effects rather than small-molecule ligands
• Druggability: ProteinsPlus_predict_binding_sites

COMPUTE, DON'T DESCRIBE

When 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.

Domain Reasoning

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.

Tool Inventory

PDB (RCSB)

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)

PDB (PDBe)

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)

PDBe PISA

PDBePISA_get_interfaces (pdb_id), PDBePISA_get_assemblies (pdb_id)

AlphaFold

alphafold_get_prediction (qualifier=UniProt), alphafold_get_summary (qualifier), alphafold_get_annotations (qualifier)

Binding Sites

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

Foldseek_search_structure (sequence, mode="tmalign"), Foldseek_get_result (ticket)

GPCRdb

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

SAbDab_search_structures (query/antigen), SAbDab_get_structure (pdb_id), TheraSAbDab_search_therapeutics (query), TheraSAbDab_search_by_target (target)

Domains

InterPro_get_protein_domains (uniprot_id), Pfam_get_protein_annotations (uniprot_id), UniProt_get_entry_by_accession (accession)

Proteomics

ProteomeXchange_search_datasets (query), ProteomeXchange_get_dataset (dataset_id)

Workflow 1: Find All Structures for a Drug Target

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.

Workflow 2: Identify Binding Pocket Ligands

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.

Workflow 3: Cross-Validate Drug Binding

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 Parameter Gotchas

Evidence Grading

Interpretation

DoGSiteScorer >0.6 = druggable; <0.4 = unlikely druggable. PISA assemblies should be cross-validated with SEC-MALS/native MS.

Limitations

• BindingDB: 60s+ for popular targets
• AlphaFold: lacks ligand context
• GPCRdb: Class A-F GPCRs only
• PDBePISA: operation is internal, not a public parameter