tooluniverse-protein-structure-retrieval - Claude MCP Skill

# 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

```python
# 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.

```python
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:

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

---

## 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)