tooluniverse-protein-structure-retrieval-6dbaae — independently scanned and version-tracked by SaferSkills.
SaferSkills independently audited tooluniverse-protein-structure-retrieval-6dbaae (Agent Skill) and scored it 100/100 (green). The audit ran 55 deterministic rules across Security, Supply Chain, Maintenance, Transparency, and Community; it found 0 high-severity and 0 lower-severity findings. The full rule-by-rule trace and per-finding evidence are below. Free, methodology-open.
Findings & checks · 0 flagged
Every scanned point with the score it earned and what moved between them.
First recorded scan — no prior version to compare against.
The primary manifest — the file an agent reads to learn what this artifact does.
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.
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.
Phase 0: Clarify (if needed) → Phase 1: Disambiguate Protein → Phase 2: Retrieve Structures → Phase 3: ReportAsk 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.
# By PDB ID: direct retrieval
# By UniProt: get AlphaFold + search experimental structures
af_structure = tu.tools.alphafold_get_prediction(uniprot_id=uniprot_id)
# By protein name: search
result = tu.tools.PDBeSearch_search_structures(query=protein_name)Retrieve silently. Do NOT narrate the process.
pdb_id = "4INS"
# Search, metadata, quality, ligands, similar structures
result = 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 entries
entries = 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 data
summary = 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)| 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 |
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.
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 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.
Present as a Structure Profile Report. Hide search process. Include:
| 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 |
<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.
>90: very high, experimental-like. 70-90: good backbone. 50-70: uncertain/flexible. <50: likely disordered.
| 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 |
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)
~30 seconds. Free. No account. Every finding cites a rule and a line of evidence.