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Integrate structural biology data with proteomics for drug target validation. Retrieves protein structures from PDB (RCSB, PDBe), AlphaFold predictions, antibody structures (SAbDab), GPCR data (GPCRdb), binding pocket analysis (ProteinsPlus), and ligand interactions (BindingDB). Use when asked to find structures for a drug target, identify binding site ligands, cross-validate drug binding with structural data, assess structural druggability, or compare experimental vs predicted structures.
npx skill4agent add mims-harvard/tooluniverse tooluniverse-structural-proteomicsPDBeSIFTS_get_best_structuresRCSBGraphQL_get_structure_summaryalphafold_get_summaryPDBe_get_structure_ligandsBindingDB_get_ligands_by_uniprotProteinsPlus_predict_binding_sitesRCSBAdvSearch_search_structuresRCSBData_get_entryRCSBGraphQL_get_structure_summaryRCSBGraphQL_get_ligand_infoRCSB_get_chemical_componentpdbe_get_entry_summaryPDBe_get_structure_ligandsPDBe_get_bound_moleculesPDBeSearch_search_structuresPDBeSIFTS_get_best_structuresPDBeSIFTS_get_all_structuresPDBe_KB_get_ligand_sitesPDBe_KB_get_interface_residuesPDBeValidation_get_quality_scoresPDBePISA_get_interfacesPDBePISA_get_assembliesalphafold_get_predictionalphafold_get_summaryalphafold_get_annotationsProteinsPlus_predict_binding_sitesBindingDB_get_ligands_by_uniprotBindingDB_get_ligands_by_pdbBindingDB_get_targets_by_compoundFoldseek_search_structureFoldseek_get_resultGPCRdb_get_proteinGPCRdb_get_structuresGPCRdb_get_ligandsGPCRdb_get_mutations{symbol.lower()}_humanSAbDab_search_structuresSAbDab_get_structureTheraSAbDab_search_therapeuticsTheraSAbDab_search_by_targetInterPro_get_protein_domainsPfam_get_protein_annotationsUniProt_get_entry_by_accessionProteomeXchange_search_datasetsProteomeXchange_get_datasetPhase 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)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 ligandsPhase 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 |
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| gene symbol | |
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| 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) |
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