protein_structure_analysis

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

{
    "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.

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())