tooluniverse-protein-structure-retrieval - Claude MCP Skill

# 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

```python
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

```python
# 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:

```python
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

```python
# 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

```python
# 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.

```markdown
# Protein Structure Profile: [Protein Name]

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

---

## Best Available Structure

### [PDB ID]: [Title]

| Attribute | Value |
|-----------|-------|
| **PDB ID** | [pdb_id] |
| **UniProt** | [uniprot_id] |
| **Organism** | [species] |
| **Method** | X-ray / Cryo-EM / NMR |
| **Resolution** | [X.XX] Å |
| **Release Date** | [date] |

**Quality Assessment**: ●●● High / ●●○ Medium / ●○○ Low

### Experimental Details
| Parameter | Value |
|-----------|-------|
| **Method** | [X-ray crystallography] |
| **Resolution** | [1.9 Å] |
| **R-factor** | [0.18] |
| **R-free** | [0.21] |
| **Space Group** | [P 21 21 21] |

### Structure Composition
| Component | Count | Details |
|-----------|-------|---------|
| **Chains** | [N] | [A (enzyme), B (inhibitor)] |
| **Residues** | [N] | [coverage %] |
| **Ligands** | [N] | [list ligand names] |
| **Waters** | [N] | |
| **Metals** | [N] | [Zn, Mg, etc.] |

### Bound Ligands
| Ligand ID | Name | Type | Binding Site |
|-----------|------|------|--------------|
| [ATP] | Adenosine triphosphate | Substrate | Active site |
| [MG] | Magnesium ion | Cofactor | Catalytic |

### 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] ų
- Druggability: High/Medium/Low

---

## Alternative Structures

Ranked by quality and relevance:

| Rank | PDB ID | Resolution | Method | Ligands | Notes |
|------|--------|------------|--------|---------|-------|
| 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 |
|-----------|-------|
| **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

---

## Structure Comparison

| Property | [PDB_1] | [PDB_2] | AlphaFold |
|----------|---------|---------|-----------|
| 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

### Coordinate Files
| Format | PDB ID | Link |
|--------|--------|------|
| PDB | [4INS] | [link] |
| mmCIF | [4INS] | [link] |
| AlphaFold | [UniProt] | [link] |

### 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 |