Tooluniverse Protein Structure Retrieval

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: Clarify (if needed) → Phase 1: Disambiguate Protein → Phase 2: Retrieve Structures → Phase 3: Report

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

# By PDB ID: direct retrieval# By UniProt: get AlphaFold + search experimental structuresaf_structure = tu.tools.alphafold_get_prediction(uniprot_id=uniprot_id)# By protein name: searchresult = tu.tools.PDBeSearch_search_structures(query=protein_name)

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.

pdb_id = "4INS"
# Search, metadata, quality, ligands, similar structuresresult = tu.tools.PDBeSearch_search_structures(query=name)metadata = tu.tools.get_protein_metadata_by_pdb_id(pdb_id=pdb_id)exp = tu.tools.RCSBData_get_entry(pdb_id=pdb_id)quality = tu.tools.PDBeValidation_get_quality_scores(pdb_id=pdb_id)ligands = tu.tools.PDBe_get_structure_ligands(pdb_id=pdb_id)  # data.ligands[]similar = tu.tools.PDB_search_similar_structures(query=pdb_id, search_type="structure")  # data.results[] with rank, score# By UniProt accession: all PDB entries, and ligand-binding residues across entriesentries = tu.tools.PDBeSIFTS_get_all_structures(uniprot_accession=uniprot_id)  # data.pdb_entries[]sites = tu.tools.PDBe_KB_get_ligand_sites(uniprot_accession=uniprot_id)  # data.ligands[]
# PDBe additional datasummary = tu.tools.pdbe_get_entry_summary(pdb_id=pdb_id)molecules = tu.tools.pdbe_get_entry_molecules(pdb_id=pdb_id)
# AlphaFold (when no experimental structure, or for comparison)af = tu.tools.alphafold_get_prediction(uniprot_id=uniprot_id)

Fallback Chains

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

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

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)