mims-harvard/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
• 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.

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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)

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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

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Tool Parameter Gotchas

| 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 |

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Evidence Grading

| 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 |

Interpretation

| 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.

Limitations

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