tooluniverse-protein-structure-retrieval
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, structure-quality comparison, and selecting structures for drug design or modeling.
Install
npx skills add https://github.com/mims-harvard/tooluniverse --skill tooluniverse-protein-structure-retrievalProtein 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 structures
af_structure = tu.tools.alphafold_get_prediction(uniprot_id=uniprot_id)
# By protein name: search
result = tu.tools.PDBeSearch_search_structures(protein_name=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 structures
result = tu.tools.PDBeSearch_search_structures(protein_name=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_KB_get_ligand_sites(pdb_id=pdb_id)
similar = tu.tools.PDBeSIFTS_get_all_structures(pdb_id=pdb_id, cutoff=2.0)
# 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)
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:
- Search Summary: query, organism, experimental + AlphaFold structure counts
- Best Structure: PDB ID, UniProt, organism, method, resolution, date, quality assessment
- Experimental Details: method, resolution, R-factor, R-free, space group
- Composition: chains, residues (coverage%), ligands, waters, metals
- Bound Ligands: ligand ID, name, type, binding site
- Binding Site Details (for drug discovery): location, key residues, druggability
- Alternative Structures: ranked by quality with resolution, method, ligands
- AlphaFold Prediction: UniProt, model version, pLDDT confidence distribution, use cases
- Structure Comparison: resolution, completeness, ligands across structures
- 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)