tooluniverse-protein-structure-prediction - Claude MCP Skill

# Protein Structure Prediction and Analysis

End-to-end workflow for protein structure prediction starting from a sequence or UniProt accession. Combines ESMFold de novo prediction, AlphaFold database retrieval, experimental structure benchmarking from RCSB, ProtVar variant impact assessment, and ProtParam sequence property calculation.

**KEY PRINCIPLES**:
1. **Sequence first** — obtain or verify the protein sequence before prediction
2. **ESMFold for fast de novo** — works directly on sequence (up to ~800 residues); no database lookup needed
3. **AlphaFold for reference** — retrieve precomputed AlphaFold model for comparison; use `qualifier` parameter (UniProt accession)
4. **Quality before interpretation** — always report pLDDT scores; do not interpret low-confidence regions as folded
5. **Experimental validation** — compare predictions to RCSB experimental structures when available
6. **ProtVar for variants** — use when the question involves mutations or SNVs affecting structure
7. **English-first queries** — use English protein names in all tool calls; respond in the user's language

## LOOK UP, DON'T GUESS
When uncertain about any scientific fact, SEARCH databases first rather than reasoning from memory. A database-verified answer is always more reliable than a guess.

---

## COMPUTE, DON'T DESCRIBE
When analysis requires computation (statistics, data processing, scoring, enrichment), write and run Python code via Bash. Don't describe what you would do — execute it and report actual results. Use ToolUniverse tools to retrieve data, then Python (pandas, scipy, statsmodels, matplotlib) to analyze it.

## When to Use

Apply when users ask:
- "Predict the structure of this sequence: [FASTA]"
- "What does the AlphaFold model for [protein] look like?"
- "How confident is the AlphaFold prediction for [protein]?"
- "Is there an experimental structure for [protein] and how does it compare to AlphaFold?"
- "How does mutation [variant] affect the structure of [protein]?"
- "What are the physicochemical properties of [protein] sequence?"
- "Predict the structure of this novel protein" / "I have a new sequence, can you model it?"

**Not for** (use `tooluniverse-protein-structure-retrieval` instead): retrieval-only tasks where user provides a PDB ID or wants to browse experimental structures without prediction.

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## Input Parameters

| Parameter | Required | Description | Example |
|-----------|----------|-------------|---------|
| **sequence** | Yes (for ESMFold) | Amino acid sequence (single-letter FASTA) | `MVLSPADKTNVK...` |
| **uniprot_id** | Yes (for AlphaFold) | UniProt accession | `P04637`, `P69905` |
| **variant** | No | Variant notation for structural impact | `P04637 R175H`, `TP53 R175H` |
| **max_length** | No | ESMFold limit: ~800 residues recommended | — |

---

## Workflow Overview

```
Phase 0: Input preparation (sequence retrieval if needed)
    |
Phase 1: Sequence properties (ProtParam_calculate)
    |
Phase 2: De novo prediction (ESMFold_predict_structure)
    |
Phase 3: AlphaFold reference (alphafold_get_prediction + alphafold_get_summary)
    |
Phase 4: Experimental structure comparison (RCSBAdvSearch_search_structures, RCSBData_get_entry)
    |
Phase 5: Variant structural impact (ProtVar_map_variant + ProtVar_get_function) [if variant provided]
    |
Phase 6: Quality synthesis and interpretation
```

---

## Phase 0: Input Preparation

**Objective**: Obtain or verify the protein sequence needed for ESMFold prediction.

### If sequence is already provided

Use it directly for `ESMFold_predict_structure`. Check length:
- 1-400 residues: full prediction, high confidence expected
- 400-800 residues: prediction supported, may be slower
- >800 residues: ESMFold may fail or produce lower quality; recommend using AlphaFold instead

### If only protein name or UniProt ID is provided

Retrieve sequence from `UniProt_get_entry_by_accession`:
- `accession`: UniProt accession
- Extract the `sequence.value` field from the response

**Note**: If only a name is given (not accession), first resolve with `UniProt_search` or `MyGene_query_genes` to get the UniProt accession, then fetch the sequence.

---

## Phase 1: Sequence Properties

**Objective**: Calculate physicochemical properties before prediction to contextualize results.

### Tools

**ProtParam_calculate**:
- `sequence`: amino acid sequence string (single-letter code)
- Returns: molecular weight, isoelectric point (pI), extinction coefficient, instability index, GRAVY score, amino acid composition

### Key Properties to Report

- **Molecular weight** — size context
- **Isoelectric point (pI)** — charge at neutral pH
- **Instability index** — >40 suggests unstable protein; affects prediction quality
- **GRAVY score** — hydrophobicity; >0 indicates membrane association tendency
- **Length** — determines ESMFold feasibility

---

## Phase 2: De Novo Structure Prediction (ESMFold)

**Objective**: Predict 3D structure from sequence using Meta's ESM-2 language model.

### Tools

**ESMFold_predict_structure**:
- `sequence`: amino acid sequence string
- Returns: predicted structure in PDB format, per-residue pLDDT confidence scores, pTM score (global fold confidence)

### Workflow

1. Call `ESMFold_predict_structure` with the sequence
2. Parse pLDDT scores:
   - Per-residue confidence array
   - Compute mean pLDDT over all residues
   - Identify low-confidence regions (pLDDT < 50)
3. Parse pTM score (predicted Template Modeling score) — overall fold quality
4. Record the PDB-format coordinate output for downstream visualization

### Quality Interpretation

| pLDDT Range | Interpretation | Reliability |
|-------------|---------------|-------------|
| >90 | Very high confidence | Equivalent to experimental quality |
| 70-90 | High confidence | Backbone reliable, side chains approximate |
| 50-70 | Low confidence | Potentially disordered or flexible region |
| <50 | Very low confidence | Likely intrinsically disordered; do not interpret |

| pTM Score | Fold Confidence |
|-----------|----------------|
| >0.8 | High confidence global fold |
| 0.5-0.8 | Moderate; some domains may be uncertain |
| <0.5 | Low global fold confidence |

### ESMFold vs AlphaFold

- ESMFold: faster, works directly on sequence, good for novel sequences, no database lookup
- AlphaFold: uses multiple sequence alignment (MSA); typically higher accuracy for well-conserved proteins
- Both predict single-chain monomer structures (not complexes in standard mode)

---

## Phase 3: AlphaFold Reference Model

**Objective**: Retrieve precomputed AlphaFold2 model for comparison and higher-accuracy reference.

### Tools

**alphafold_get_prediction**:
- `qualifier` (or alias `uniprot_id` / `uniprot_accession`): UniProt accession (e.g., `"P04637"`)
- Returns: AlphaFold model URL, pLDDT scores, model version

**alphafold_get_summary**:
- `qualifier` (or alias `uniprot_id` / `uniprot_accession`): UniProt accession
- Returns: prediction summary including confidence metrics, model quality

**alphafold_get_annotations** (optional):
- `qualifier`: UniProt accession
- Returns: functional region annotations overlaid on structure (binding sites, active sites)

**AlphaFill_get_transplants** (optional, ligands/cofactors):
- `uniprot`: UniProt accession (e.g., `"P00520"` ABL1)
- Returns: ligands, cofactors, and ions transplanted onto the AlphaFold model by homology, with per-transplant local RMSD and source PDB IDs
- When to use it: the apo AlphaFold model omits bound ligands/metals; run this to recover the likely cofactor/ligand/ion environment (e.g., ABL1 → STI/imatinib) for structure-guided binding-site interpretation

### Workflow

1. Call `alphafold_get_prediction` and `alphafold_get_summary`
2. Extract mean pLDDT and per-residue confidence
3. Compare ESMFold vs AlphaFold pLDDT profiles:
   - Do they agree on low-confidence regions?
   - Large differences may indicate disordered/flexible regions
4. Note the AlphaFold model version (v1/v2/v3/v4)

### Decision Logic

- If no UniProt accession available: skip AlphaFold; use ESMFold only
- If protein is a complex or has multiple chains: note that both tools predict single chains
- If AlphaFold confidence is very high (mean pLDDT > 85): recommend using AlphaFold as primary reference

---

## Phase 4: Experimental Structure Comparison

**Objective**: Check whether experimental structures exist in PDB and how predictions compare.

### Tools

**RCSBAdvSearch_search_structures** (search by protein/gene name):
- `query`: protein name or gene symbol
- `limit`: number of results (default 10)
- Returns: list of PDB entries with resolution, method, title

**RCSBData_get_entry** (details for a specific PDB ID):
- `pdb_id`: 4-character PDB identifier
- Returns: metadata including method, resolution, chains, ligands, release date

### Workflow

1. Search for experimental structures using protein name
2. Filter for highest-resolution X-ray or cryo-EM structures
3. For the best experimental structure, retrieve entry details
4. Compare to predictions:
   - If experimental structure exists: note coverage, resolution, method
   - Flag regions predicted with high confidence but missing from experimental structure (could be disordered in crystal)
   - Flag regions in experimental structure with low pLDDT (may be crystal artifacts vs true fold)

### Fallback

- If RCSB search returns no results: note "no experimental structure found in PDB" and proceed with predictions only
- Suggest checking PDBe as secondary source

---

## Phase 5: Variant Structural Impact (When Variant Provided)

**Objective**: Assess how a specific amino acid substitution affects the predicted structure.

### Tools

**ProtVar_map_variant**:
- `variant`: string notation like `"P04637 R175H"` or HGVS notation
- Returns: mapped residue position, genomic coordinates, consequence type, variant accession

**ProtVar_get_function**:
- `accession`: UniProt accession
- `position`: integer residue position
- `variant_aa`: mutant amino acid (single letter)
- Returns: functional annotations — domain, active site, binding site, conservation score, clinical significance, predicted pathogenicity

### Workflow

1. Call `ProtVar_map_variant` to resolve the variant and confirm position
2. Call `ProtVar_get_function` with wild-type position to get domain context
3. Assess: is the mutated residue in a critical structural region?
   - Active site / binding site: likely high functional impact
   - Buried hydrophobic core: likely destabilizes fold
   - Surface-exposed, disordered region: less likely to affect overall fold
4. Compare pLDDT at that position (from ESMFold/AlphaFold) to assess if the region is well-predicted

### Evidence Grading for Variant Impact

| Tier | Evidence |
|------|----------|
| T1 | Clinical/functional data for this exact variant (from ProtVar) |
| T2 | Variant at experimentally characterized active site or binding interface |
| T3 | Computational pathogenicity prediction (PolyPhen, SIFT from ProtVar) |
| T4 | Position in predicted structured region only |

---

## Phase 6: Quality Synthesis and Report

### Required Report Sections

1. **Protein summary** — name, length, pI, stability index (from ProtParam)
2. **Structure prediction summary table**:
   | Method | Mean pLDDT | pTM/Global Score | Coverage | Notes |
   |--------|-----------|------------------|----------|-------|
   | ESMFold | X.X | X.X | 100% (full seq) | — |
   | AlphaFold | X.X | — | 100% | version vN |
   | Experimental (best) | N/A | N/A | XX% | PDB: XXXX, Xray, X.X A |

3. **Confidence map** — regions of high vs low confidence; highlight disordered regions
4. **Experimental structure comparison** — does PDB have coverage? How does prediction align?
5. **Variant impact** (if applicable) — domain context, pathogenicity, structural consequence
6. **Recommendations**:
   - Which model to use for downstream applications (docking, design, etc.)
   - Regions to treat as unreliable
   - Suggested experimental validation approaches

### Quality Minimums

- Report mean pLDDT for both ESMFold and AlphaFold
- Identify all low-confidence regions (pLDDT < 50) by residue range
- Check PDB for experimental structures (at minimum 1 search query)
- Compare at least 2 prediction sources when UniProt accession is available

---

## Tool Parameter Reference

| Tool | Key Parameter | Notes |
|------|--------------|-------|
| `ESMFold_predict_structure` | `sequence` | Raw amino acid string, no spaces, no FASTA header |
| `alphafold_get_prediction` | `qualifier` or `uniprot_id` | UniProt accession (e.g., `"P04637"`) |
| `alphafold_get_summary` | `qualifier` or `uniprot_id` | Same UniProt accession |
| `ProtParam_calculate` | `sequence` | Same sequence string |
| `ProtVar_map_variant` | `variant` | Format: `"<UniProt_ID> <AA><pos><AA>"` e.g., `"P04637 R175H"` |
| `ProtVar_get_function` | `position` | Integer residue number |

---

## Fallback Strategies

| Situation | Fallback |
|-----------|----------|
| ESMFold fails (sequence too long > 800 aa) | Use AlphaFold model only; note length limitation |
| AlphaFold no entry for UniProt ID | Use ESMFold prediction only |
| RCSB search returns no results | Note no experimental structure; proceed with predictions |
| No UniProt accession available | Use ESMFold from raw sequence; skip AlphaFold |
| ProtVar variant not found | Manually assess position from domain annotation in Phase 4 |

---

## Databases Integrated

| Database | Coverage | What it provides |
|----------|----------|-----------------|
| **ESMFold** | Any protein sequence (up to ~800 aa) | De novo structure prediction from sequence alone |
| **AlphaFold DB** | UniProt reviewed proteins (>200M entries) | Precomputed predictions with per-residue pLDDT |
| **RCSB PDB** | ~220,000 experimental structures | Ground-truth experimental coordinates for comparison |
| **ProtVar** | All UniProt proteins | Variant impact, domain context, clinical annotations |
| **ProtParam** | Any sequence | Physicochemical sequence properties |

---

## Limitations

- **ESMFold length limit**: sequences longer than ~800 residues may fail or have reduced quality
- **Single-chain only**: both ESMFold and standard AlphaFold predict monomers; complex prediction requires AlphaFold-Multimer (not available via these tools)
- **Disordered regions**: pLDDT < 50 indicates intrinsically disordered regions (IDRs) — do not interpret these as structured
- **No dynamics**: predicted structures are static; do not represent conformational flexibility or allosteric changes
- **Novel folds**: ESMFold may struggle with proteins having no homologs in training data
- **AlphaFold DB coverage**: some recently characterized proteins may not yet be in the AlphaFold database