Protein Structure Analysis

---
name: protein_structure_analysis
description: "Protein Structure Comprehensive Analysis - Comprehensive structure analysis: download PDB, extract chains, calculate geometry, quality metrics, and composition. Use this skill for structural biology tasks involving retrieve protein data by pdbcode extract pdb chains calculate pdb structural geometry calculate pdb quality metrics calculate pdb composition info. Combines 5 tools from 1 SCP server(s)."
---

# Protein Structure Comprehensive Analysis

**Discipline**: Structural Biology | **Tools Used**: 5 | **Servers**: 1

## Description

Comprehensive structure analysis: download PDB, extract chains, calculate geometry, quality metrics, and composition.

## Tools Used

- **`retrieve_protein_data_by_pdbcode`** from `server-2` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool`
- **`extract_pdb_chains`** from `server-2` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool`
- **`calculate_pdb_structural_geometry`** from `server-2` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool`
- **`calculate_pdb_quality_metrics`** from `server-2` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool`
- **`calculate_pdb_composition_info`** from `server-2` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool`

## Workflow

1. Download PDB structure
2. Extract chain sequences
3. Calculate structural geometry
4. Assess quality metrics
5. Analyze composition

## Test Case

### Input
```json
{
    "pdb_code": "1AKE"
}
```

### Expected Steps
1. Download PDB structure
2. Extract chain sequences
3. Calculate structural geometry
4. Assess quality metrics
5. Analyze composition

## Usage Example

> **Note:** Replace `<YOUR_SCP_HUB_API_KEY>` with your own SCP Hub API Key. You can obtain one from the [SCP Platform](https://scphub.intern-ai.org.cn).

```python
import asyncio
import json
from mcp import ClientSession
from mcp.client.streamable_http import streamablehttp_client
from mcp.client.sse import sse_client

SERVERS = {
    "server-2": "https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool"
}

async def connect(url, transport_type):
    transport = streamablehttp_client(url=url, headers={"SCP-HUB-API-KEY": "<YOUR_SCP_HUB_API_KEY>"})
    read, write, _ = await transport.__aenter__()
    ctx = ClientSession(read, write)
    session = await ctx.__aenter__()
    await session.initialize()
    return session, ctx, transport

def parse(result):
    try:
        if hasattr(result, 'content') and result.content:
            c = result.content[0]
            if hasattr(c, 'text'):
                try: return json.loads(c.text)
                except: return c.text
        return str(result)
    except: return str(result)

async def main():
    # Connect to required servers
    sessions = {}
    sessions["server-2"], _, _ = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool", "streamable-http")

    # Execute workflow steps
    # Step 1: Download PDB structure
    result_1 = await sessions["server-2"].call_tool("retrieve_protein_data_by_pdbcode", arguments={})
    data_1 = parse(result_1)
    print(f"Step 1 result: {json.dumps(data_1, indent=2, ensure_ascii=False)[:500]}")

    # Step 2: Extract chain sequences
    result_2 = await sessions["server-2"].call_tool("extract_pdb_chains", arguments={})
    data_2 = parse(result_2)
    print(f"Step 2 result: {json.dumps(data_2, indent=2, ensure_ascii=False)[:500]}")

    # Step 3: Calculate structural geometry
    result_3 = await sessions["server-2"].call_tool("calculate_pdb_structural_geometry", arguments={})
    data_3 = parse(result_3)
    print(f"Step 3 result: {json.dumps(data_3, indent=2, ensure_ascii=False)[:500]}")

    # Step 4: Assess quality metrics
    result_4 = await sessions["server-2"].call_tool("calculate_pdb_quality_metrics", arguments={})
    data_4 = parse(result_4)
    print(f"Step 4 result: {json.dumps(data_4, indent=2, ensure_ascii=False)[:500]}")

    # Step 5: Analyze composition
    result_5 = await sessions["server-2"].call_tool("calculate_pdb_composition_info", arguments={})
    data_5 = parse(result_5)
    print(f"Step 5 result: {json.dumps(data_5, indent=2, ensure_ascii=False)[:500]}")

    # Cleanup
    print("Workflow complete!")

if __name__ == "__main__":
    asyncio.run(main())
```