Protein Structure Data Retrieval
Retrieve protein structures with proper disambiguation, quality assessment, and comprehensive metadata.
IMPORTANT: Always use English terms in tool calls (protein names, organism names), even if the user writes in another language. Only try original-language terms as a fallback if English returns no results. Respond in the user's language. Workflow Overview Phase 0: Clarify (if needed) ↓ Phase 1: Disambiguate Protein Identity ↓ Phase 2: Retrieve Structures (Internal) ↓ Phase 3: Report Structure Profile Phase 0: Clarification (When Needed) Ask the user ONLY if: Protein name matches multiple genes/families (e.g., "kinase" → which kinase?) Organism not specified for conserved proteins Intent unclear: need experimental structure vs AlphaFold prediction? Skip clarification for: Specific PDB IDs (4-character codes) UniProt accessions Unambiguous protein names with organism Phase 1: Protein Disambiguation 1.1 Resolve Protein Identity from tooluniverse import ToolUniverse tu = ToolUniverse ( ) tu . load_tools ( )

Strategy depends on input type

if user_provided_pdb_id :

Direct structure retrieval

pdb_id

user_provided_pdb_id . upper ( ) elif user_provided_uniprot :

Get UniProt info, then search structures

uniprot_id

user_provided_uniprot

Can also get AlphaFold structure

af_structure

tu . tools . alphafold_get_structure_by_uniprot ( uniprot_id = uniprot_id ) elif user_provided_protein_name :

Search by name

result

tu . tools . search_structures_by_protein_name ( protein_name = protein_name ) 1.2 Identity Resolution Checklist Protein name/gene identified Organism confirmed UniProt accession (if available) Isoform/variant specified (if relevant) 1.3 Handle Naming Collisions Common ambiguous terms: Term Ambiguity Resolution "kinase" Hundreds of kinases Ask which kinase (EGFR, CDK2, etc.) "receptor" Many receptor types Specify receptor family "protease" Multiple families Ask serine/cysteine/metallo/etc. "hemoglobin" Clear Proceed (α/β chain specified if needed) "insulin" Clear Proceed Phase 2: Data Retrieval (Internal) Retrieve all data silently. Do NOT narrate the search process. 2.1 Search Structures

Search by protein name

result

tu . tools . search_structures_by_protein_name ( protein_name = protein_name )

Filter results by quality

high_res

[ entry for entry in result [ "data" ] if entry . get ( "resolution" ) and entry [ "resolution" ] < 2.5 ] 2.2 Get Structure Details For each relevant structure: pdb_id = "4INS"

Basic metadata

metadata

tu . tools . get_protein_metadata_by_pdb_id ( pdb_id = pdb_id )

Experimental details

exp_details

tu . tools . get_protein_experimental_details_by_pdb_id ( pdb_id = pdb_id )

Resolution (if X-ray)

resolution

tu . tools . get_protein_resolution_by_pdb_id ( pdb_id = pdb_id )

Bound ligands

ligands

tu . tools . get_protein_ligands_by_pdb_id ( pdb_id = pdb_id )

Similar structures

similar

tu . tools . get_similar_structures_by_pdb_id ( pdb_id = pdb_id , cutoff = 2.0 ) 2.3 PDBe Additional Data

Entry summary

summary

tu . tools . pdbe_get_entry_summary ( pdb_id = pdb_id )

Molecular entities

molecules

tu . tools . pdbe_get_molecules ( pdb_id = pdb_id )

Binding sites

binding_sites

tu . tools . pdbe_get_binding_sites ( pdb_id = pdb_id ) 2.4 AlphaFold Predictions

When no experimental structure exists, or for comparison

if uniprot_id : af_structure = tu . tools . alphafold_get_structure_by_uniprot ( uniprot_id = uniprot_id ) Fallback Chains Primary Fallback Notes RCSB search PDBe search Regional availability get_protein_metadata pdbe_get_entry_summary Alternative source Experimental structure AlphaFold prediction No experimental structure get_protein_ligands pdbe_get_binding_sites Ligand info unavailable Phase 3: Report Structure Profile Output Structure Present as a Structure Profile Report . Hide search process.

Protein Structure Profile: [Protein Name] ** Search Summary ** - Query: [protein name/PDB ID] - Organism: [species] - Structures Found: [N] experimental, [M] AlphaFold

Best Available Structure

| Attribute | Value | |

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PDB ID
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[pdb_id]
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UniProt
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[uniprot_id]
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Organism
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[species]
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Method
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X-ray / Cryo-EM / NMR
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Resolution
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[X.XX] Å
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Release Date
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[date]
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Quality Assessment
**: ●●● High / ●●○ Medium / ●○○ Low

Experimental Details | Parameter | Value | |

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Binding Site Details For drug discovery applications: ** Site 1: Active Site ** - Location: Chain A, residues 45-89 - Key residues: Asp45, Glu67, His89 - Pocket volume: [X] Å³ - Druggability: High/Medium/Low

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| | 1 | [4INS] | 1.9 Å | X-ray | Zn | Best resolution | | 2 | [3I40] | 2.1 Å | X-ray | Zn, phenol | With inhibitor | | 3 | [1TRZ] | 2.3 Å | X-ray | None | Porcine |

AlphaFold Prediction

AF-[UniProt]-F1 | Attribute | Value | |

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| | ** UniProt ** | [uniprot_id] | | ** Model Version ** | [v4] | | ** Confidence (pLDDT) ** | [average score] | ** Confidence Distribution ** : - Very High (>90): [X]% of residues - High (70-90): [X]% of residues - Low (50-70): [X]% of residues - Very Low (<50): [X]% of residues ** Use Cases ** : - ✓ Overall fold reliable - ✓ Core domain structure - ⚠ Loop regions uncertain - ✗ Not suitable for binding site analysis

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| | Resolution | 1.9 Å | 2.5 Å | N/A (predicted) | | Completeness | 98% | 85% | 100% | | Ligands | Yes | No | No | | Confidence | Experimental | Experimental | High (85 avg) |

Download Links

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Database Links

RCSB PDB: https://www.rcsb.org/structure/[pdb_id]

PDBe: https://www.ebi.ac.uk/pdbe/entry/pdb/[pdb_id]

AlphaFold: https://alphafold.ebi.ac.uk/entry/[uniprot_id] Retrieved: [date] Quality Assessment Tiers Experimental Structures Tier Symbol Criteria Excellent ●●●● X-ray <1.5Å, complete, R-free <0.22 High ●●●○ X-ray <2.0Å OR Cryo-EM <3.0Å Good ●●○○ X-ray 2.0-3.0Å OR Cryo-EM 3.0-4.0Å Moderate ●○○○ X-ray >3.0Å OR NMR ensemble Low ○○○○

4.0Å, incomplete, or problematic Resolution Guide Resolution Use Case <1.5 Å Atomic detail, H-bond analysis 1.5-2.0 Å Drug design, mechanism studies 2.0-2.5 Å Structure-based design 2.5-3.5 Å Overall architecture, fold 3.5 Å Domain arrangement only AlphaFold Confidence pLDDT Score Interpretation 90 Very high confidence, experimental-like 70-90 Good backbone confidence 50-70 Uncertain, flexible regions <50 Low confidence, likely disordered Completeness Checklist Every structure report MUST include: For Specific PDB ID (Required) PDB ID and title Experimental method Resolution (or N/A for NMR) Organism Quality assessment Download links For Protein Name Search (Required) Search summary with result count Top structures with quality ranking Best structure recommendation AlphaFold alternative (if no experimental structure) Always Include Ligand information (or "No ligands bound") Data sources with links Retrieval date Common Use Cases Drug Discovery Target User: "Get structure for EGFR kinase with inhibitor" → Filter for ligand-bound structures, emphasize binding site Model Building User: "Find best template for homology modeling of protein X" → High-resolution structures, note sequence coverage Structure Comparison User: "Compare available SARS-CoV-2 main protease structures" → All structures with systematic comparison table AlphaFold When No Experimental User: "Structure of protein with UniProt P12345" → Check PDB first, then AlphaFold, note confidence Error Handling Error Response "PDB ID not found" Verify 4-character format, check if obsoleted "No structures for protein" Offer AlphaFold prediction, suggest similar proteins "Download failed" Retry once, provide alternative link "Resolution unavailable" Likely NMR/model, note in assessment Tool Reference RCSB PDB (Experimental Structures) Tool Purpose search_structures_by_protein_name Name-based search get_protein_metadata_by_pdb_id Basic info get_protein_experimental_details_by_pdb_id Method details get_protein_resolution_by_pdb_id Quality metric get_protein_ligands_by_pdb_id Bound molecules download_pdb_structure_file Coordinate files get_similar_structures_by_pdb_id Homologs PDBe (European PDB) Tool Purpose pdbe_get_entry_summary Overview pdbe_get_molecules Molecular entities pdbe_get_experiment_info Experimental data pdbe_get_binding_sites Ligand pockets AlphaFold (Predictions) Tool Purpose alphafold_get_structure_by_uniprot Get prediction alphafold_search_structures Search predictions

安装

Strategy depends on input type

Direct structure retrieval

pdb_id

Get UniProt info, then search structures

uniprot_id

Can also get AlphaFold structure

af_structure

Search by name

result

Search by protein name

result

Filter results by quality

high_res

Basic metadata

metadata

Experimental details

exp_details

Resolution (if X-ray)

resolution

Bound ligands

ligands

Similar structures

similar

Entry summary

summary

Molecular entities

molecules

Binding sites

binding_sites

When no experimental structure exists, or for comparison

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Database Links

RCSB PDB: https://www.rcsb.org/structure/[pdb_id]

PDBe: https://www.ebi.ac.uk/pdbe/entry/pdb/[pdb_id]