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 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)
1---2name: tooluniverse-protein-structure-retrieval3description: 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.4---5
6# Protein Structure Data Retrieval
7
8Retrieve protein structures with disambiguation, quality assessment, and comprehensive metadata.
9
10**IMPORTANT**: Always use English terms in tool calls. Respond in the user's language.
11
12**LOOK UP DON'T GUESS**: Never assume PDB IDs, resolution, or availability. Always query RCSB/PDBe and AlphaFold to confirm.
13
14## Domain Reasoning
15
16Not 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.
17
18## Workflow
19
20```
21Phase 0: Clarify (if needed) → Phase 1: Disambiguate Protein → Phase 2: Retrieve Structures → Phase 3: Report
22```
23
24---
25
26## Phase 0: Clarification (When Needed)
27
28Ask ONLY if: protein name ambiguous (e.g., "kinase"), organism not specified, unclear if experimental vs AlphaFold needed.
29Skip for: specific PDB IDs, UniProt accessions, unambiguous protein+organism.
30
31---
32
33## Phase 1: Protein Disambiguation
34
35```python
36# By PDB ID: direct retrieval
37# By UniProt: get AlphaFold + search experimental structures
38af_structure = tu.tools.alphafold_get_prediction(uniprot_id=uniprot_id)
39# By protein name: search
40result = tu.tools.PDBeSearch_search_structures(protein_name=protein_name)
41```
42
43### Identity Checklist
44- Protein name/gene identified, organism confirmed
45- UniProt accession (if available), isoform/variant specified (if relevant)
46
47---
48
49## Phase 2: Data Retrieval (Internal)
50
51Retrieve silently. Do NOT narrate the process.
52
53```python
54pdb_id = "4INS"
55
56# Search, metadata, quality, ligands, similar structures
57result = tu.tools.PDBeSearch_search_structures(protein_name=name)
58metadata = tu.tools.get_protein_metadata_by_pdb_id(pdb_id=pdb_id)
59exp = tu.tools.RCSBData_get_entry(pdb_id=pdb_id)
60quality = tu.tools.PDBeValidation_get_quality_scores(pdb_id=pdb_id)
61ligands = tu.tools.PDBe_KB_get_ligand_sites(pdb_id=pdb_id)
62similar = tu.tools.PDBeSIFTS_get_all_structures(pdb_id=pdb_id, cutoff=2.0)
63
64# PDBe additional data
65summary = tu.tools.pdbe_get_entry_summary(pdb_id=pdb_id)
66molecules = tu.tools.pdbe_get_entry_molecules(pdb_id=pdb_id)
67
68# AlphaFold (when no experimental structure, or for comparison)
69af = tu.tools.alphafold_get_prediction(uniprot_id=uniprot_id)
70```
71
72### Fallback Chains
73
74| Primary | Fallback |
75|---------|----------|
76| RCSB search | PDBe search |
77| get_protein_metadata | pdbe_get_entry_summary |
78| Experimental structure | AlphaFold prediction |
79| get_protein_ligands | PDBe_KB_get_ligand_sites |
80
81---
82
83## Phase 3: Report Structure Profile
84
85Present as a **Structure Profile Report**. Hide search process. Include:
86
871. **Search Summary**: query, organism, experimental + AlphaFold structure counts
882. **Best Structure**: PDB ID, UniProt, organism, method, resolution, date, quality assessment
893. **Experimental Details**: method, resolution, R-factor, R-free, space group
904. **Composition**: chains, residues (coverage%), ligands, waters, metals
915. **Bound Ligands**: ligand ID, name, type, binding site
926. **Binding Site Details** (for drug discovery): location, key residues, druggability
937. **Alternative Structures**: ranked by quality with resolution, method, ligands
948. **AlphaFold Prediction**: UniProt, model version, pLDDT confidence distribution, use cases
959. **Structure Comparison**: resolution, completeness, ligands across structures
9610. **Download Links**: PDB/mmCIF/AlphaFold formats, database URLs
97
98---
99
100## Quality Assessment
101
102### Experimental Structures
103
104| Tier | Criteria |
105|------|----------|
106| Excellent | X-ray <1.5A, complete, R-free <0.22 |
107| High | X-ray <2.0A OR Cryo-EM <3.0A |
108| Good | X-ray 2.0-3.0A OR Cryo-EM 3.0-4.0A |
109| Moderate | X-ray >3.0A OR NMR ensemble |
110| Low | >4.0A, incomplete, or problematic |
111
112### Resolution Use Cases
113<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.
114
115### AlphaFold Confidence (pLDDT)
116>90: very high, experimental-like. 70-90: good backbone. 50-70: uncertain/flexible. <50: likely disordered.
117
118---
119
120## Error Handling
121
122| Error | Response |
123|-------|----------|
124| "PDB ID not found" | Verify 4-char format, check if obsoleted |
125| "No structures" | Offer AlphaFold, suggest similar proteins |
126| "Download failed" | Retry once, provide alternative link |
127| "Resolution unavailable" | Likely NMR/model, note in assessment |
128
129---
130
131## Tool Reference
132
133**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)
134
135**PDBe**: `pdbe_get_entry_summary` (overview), `pdbe_get_entry_molecules` (entities), `pdbe_get_entry_experiment` (experimental), `PDBe_KB_get_ligand_sites` (pockets)
136
137**AlphaFold**: `alphafold_get_prediction` (get prediction), `alphafold_get_summary` (search)
mims-harvard