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protein_structure_analysis

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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).

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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 sk-b04409a1-b32b-4511-9aeb-22980abdc05c with your own SCP Hub API Key. You can obtain one from the SCP Platform.

import asyncio
import json
from contextlib import AsyncExitStack
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, stack):
    transport = streamablehttp_client(url=url, headers={"SCP-HUB-API-KEY": "sk-b04409a1-b32b-4511-9aeb-22980abdc05c"})
    read, write, _ = await stack.enter_async_context(transport)
    ctx = ClientSession(read, write)
    session = await stack.enter_async_context(ctx)
    await session.initialize()
    return session

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():
    async with AsyncExitStack() as stack:
        # Connect to required servers
        sessions = {}
        sessions["server-2"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool", stack)

        # 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())