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 get structure ligands (per PDB ID) or PDBe KB get ligand sites (per UniProt accession) No usable AlphaFold model (multi domain protein, low pLDDT for a specific range) SwissModel get models filtered to that residue range — the repository holds per domain homology models AlphaFold's single full length model may not resolve well SWISS MODEL Repository (Homology Models + Re Indexed Experimental Structures) Use SwissModel get summary(uniprot id=...) for a one call "does a homology model exist and how good is it" check — it returns the single best coverage entry across everything SWISS MODEL has for that accession. Important : the "best" entry it returns can be an experimental PDB structure re indexed by UniProt residue range (verified live: for EGFR/P00533, get summary 's best model was an X RAY DIFFRACTION entry, not a homology model) — check best model.method , don't assume "best model" means "computed homology model." To get genuine computed homology models specifically, call SwissModel get models(uniprot id=..., provider="swissmodel") — provider="pdb" isolates the re indexed experimental entries instead, and omitting provider returns both. Other filters: range (residue window, useful for large multi domain proteins where one region has poor AlphaFold confidence) and template (a specific PDB template ID). SwissModel download pdb(uniprot id=..., provider=...) fetches the actual ATOM/HETATM coordinate text (not just a URL) for downstream docking/visualization — same filters as get models . SwissModel get models batch(uniprot ids=[...]) resolves up to 250 accessions in one call, useful when checking model availability across a gene list before deciding which proteins need AlphaFold/ESMFold instead. Quality metric caveat (verified live) : qmean global / qmean z score were null on every real homology model entry tested (EGFR's 2 SWISS MODEL models) — QMEAN is frequently absent, not a metric you can always rely on. Use coverage (fraction of the UniProt sequence the model spans), template (which PDB structure it was built from), and method as the more consistently populated quality signals; treat QMEAN as a bonus when present, not a required check. When to reach for SWISS MODEL vs. AlphaFold : AlphaFold (above) is the default single model reference for any UniProt reviewed protein. Reach for SWISS MODEL specifically when (a) you need multiple alternative models built from different templates to compare, (b) a large protein's AlphaFold confidence is poor in one region and a domain specific homology model with better template coverage might do better there, or (c) you're checking many accessions at once and want batch lookup rather than N separate AlphaFold calls. 3D Beacons (Meta Aggregator Across All Structure Providers) ThreeDBeacons get structure summary(accession=...) is the best FIRST call when you don't yet know which structure source has the most/best coverage for a UniProt accession — it queries PDBe, SWISS MODEL, AlphaFold DB, AlphaFill, and ModelArchive simultaneously and returns a by provider count plus a by category breakdown ( EXPERIMENTALLY DETERMINED / TEMPLATE BASED / AB INITIO ). Real example (verified live): EGFR/P00533 → total structures: 426 , by provider: {"PDBe": 412, "SWISS MODEL": 2, "AlphaFold DB": 6, "AlphaFill": 1, "ModelArchive": 5} — confirming this protein is overwhelmingly covered by experimental structures already, and that the 2 SWISS MODEL entries (Phase above) are a small fraction of what's actually available; don't stop at SWISS MODEL's own listing if 3D Beacons shows a much richer PDBe count. ThreeDBeacons get structures(accession=..., category=..., provider=..., max results=...) returns the individual structure/model records (not just counts) — filter by category or provider to narrow down before fetching detail elsewhere. ThreeDBeacons get annotations(accession=..., type=..., provider=...) maps residue level annotations (e.g. type="DOMAIN" , type="BINDING" ) onto the protein's 3D models — real example: BRCA1/P38398 with type="DOMAIN" returns real domain to residue mappings, while a type="BINDING" query on P04637 can legitimately return zero annotations ( annotation count: 0 ) — an empty result here means no such annotation exists in the aggregated sources, not a broken call. Workflow : use ThreeDBeacons get structure summary as the first orientation step for any UniProt accession, before deciding whether to drill into PDBe/RCSB (Phase 2), AlphaFold, or SWISS MODEL specifically. PDB REDO (Re Refined Experimental Structures) PDB REDO automatically re refines every X ray PDB entry with current software/parameters, often improving on the original deposition's refinement quality. PDB REDO get structure quality(pdb id=...) returns detailed refinement metrics (unit cell axes, B factors, real space/working correlation coefficients CCFFIN / CCWFIN , resolution DATARESH , completeness) for the re refined structure — real example (verified live): PDB 4hjo (an EGFR structure) → DATARESH: 2.75 , CCWFIN: 0.93 , COMPLETED: 96.9 . PDB REDO get version info(pdb id=...) returns re refinement provenance/versioning metadata for the same entry. When to use : prefer PDB REDO's re refined metrics over the original PDB deposition's stated resolution/R factors when precision matters for downstream drug design decisions — re refinement can meaningfully change R free and even correct minor model errors from the original deposition. 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 get structure ligands (ligands in an entry), PDBe KB get ligand sites (ligand binding residues for a UniProt accession), PDBeSIFTS get all structures (all PDB entries for a UniProt accession), PDB search similar structures (similar structures) 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) SWISS MODEL : SwissModel get summary (best available model, single call), SwissModel get models (list all models, filterable by range / provider / template ), SwissModel download pdb (actual coordinate text), SwissModel get models batch (up to 250 UniProt accessions in one call) 3D Beacons : ThreeDBeacons get structure summary (cross provider counts, best first call), ThreeDBeacons get structures (individual structure/model records, filterable by category / provider ), ThreeDBeacons get annotations (residue level domain/binding annotations mapped onto 3D models) PDB REDO : PDB REDO get structure quality (re refined X ray metrics), PDB REDO get version info (re refinement provenance)

tooluniverse-protein-structure-retrieval