Protein structure retrieval from RCSB PDB, PDBe, and AlphaFold with disambiguation, quality assessment (resolution, R-factor, pLDDT), and metadata. Distinguishes high-quality experimental (X-ray under 2 Angstrom) vs predicted vs medium-quality structures. Use for fetching protein structures, structu

Protein Structure Data Retrieval Retrieve protein structures with disambiguation, quality assessment, and comprehensive metadata. IMPORTANT : Always use English terms in tool calls. Respond in the user's language. LOOK UP DON'T GUESS : Never assume PDB IDs, resolution, or availability. Always query RCSB/PDBe and AlphaFold to confirm. Domain Reasoning Not all structures are equal. X ray <2 A is high quality for drug design. Cryo EM 3 4 A is good for fold but not side chains. AlphaFold is excellent for well folded domains but unreliable for disordered regions. Always check pLDDT (AlphaFold) or resolution (experimental) before drawing conclusions. Workflow Phase 0: Clarification (When Needed) Ask ONLY if: protein name ambiguous (e.g., "kinase"), organism not specified, unclear if experimental vs AlphaFold needed. Skip for: specific PDB IDs, UniProt accessions, unambiguous protein+organism. Phase 1: Protein Disambiguation Identity Checklist Protein name/gene identified, organism confirmed UniProt accession (if available), isoform/variant specified (if relevant) Phase 2: Data Retrieval (Internal) Retrieve silently. Do NOT narrate the process. Fallback Chains Primary Fallback RCSB search PDBe search get protein metadata pdbe get entry summary Experimental structure AlphaFold prediction get protein ligands PDBe KB get ligand sites Phase 3: Report Structure Profile Present as a Structure Profile Report . Hide search process. Include: 1. Search Summary : query, organism, experimental + AlphaFold structure counts 2. Best Structure : PDB ID, UniProt, organism, method, resolution, date, quality assessment 3. Experimental Details : method, resolution, R factor, R free, space group 4. Composition : chains, residues (coverage%), ligands, waters, metals 5. Bound Ligands : ligand ID, name, type, binding site 6. Binding Site Details (for drug discovery): location, key residues, druggability 7. Alternative Structures : ranked by quality with resolution, method, ligands 8. AlphaFold Prediction : UniProt, model version, pLDDT confidence distribution, use cases 9. Structure Comparison : resolution, completeness, ligands across structures 10. Download Links : PDB/mmCIF/AlphaFold formats, database URLs Quality Assessment Experimental Structures Tier Criteria Excellent X ray <1.5A, complete, R free <0.22 High X ray <2.0A OR Cryo EM <3.0A Good X ray 2.0 3.0A OR Cryo EM 3.0 4.0A Moderate X ray 3.0A OR NMR ensemble Low 4.0A, incomplete, or problematic Resolution Use Cases <1.5A: atomic detail, H bond analysis. 1.5 2.0A: drug design. 2.0 2.5A: structure based design. 2.5 3.5A: overall architecture. 3.5A: domain arrangement only. AlphaFold Confidence (pLDDT) 90: very high, experimental like. 70 90: good backbone. 50 70: uncertain/flexible. <50: likely disordered. Error Handling Error Response "PDB ID not found" Verify 4 char format, check if obsoleted "No structures" Offer AlphaFold, suggest similar proteins "Download failed" Retry once, provide alternative link "Resolution unavailable" Likely NMR/model, note in assessment Tool Reference RCSB PDB : PDBeSearch search structures (search), get protein metadata by pdb id (basic info), RCSBData get entry (details), PDBeValidation get quality scores (quality), PDBe KB get ligand sites (ligands), PDBeSIFTS get all structures (homologs) PDBe : pdbe get entry summary (overview), pdbe get entry molecules (entities), pdbe get entry experiment (experimental), PDBe KB get ligand sites (pockets) AlphaFold : alphafold get prediction (get prediction), alphafold get summary (search)

tooluniverse-protein-structure-retrieval