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

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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.

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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)

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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

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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

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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.

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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

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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)