molecular-docking-pipeline

name	molecular_docking_pipeline
description	Molecular Docking Pipeline - Complete docking workflow: retrieve protein structure, predict binding pockets, prepare receptor, and dock ligand. Use this skill for structural biology tasks involving retrieve protein data by pdbcode run fpocket convert pdb to pdbqt dock quick molecule docking. Combines 4 tools from 2 SCP server(s).

Molecular Docking Pipeline

Discipline: Structural Biology | Tools Used: 4 | Servers: 2

Description

Complete docking workflow: retrieve protein structure, predict binding pockets, prepare receptor, and dock ligand.

Tools Used

• retrieve_protein_data_by_pdbcode from server-2 (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool
• run_fpocket from server-3 (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/3/DrugSDA-Model
• convert_pdb_to_pdbqt_dock from server-2 (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool
• quick_molecule_docking from server-3 (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/3/DrugSDA-Model

Workflow

1. Download protein structure
2. Predict binding pockets
3. Prepare receptor for docking
4. Perform docking

Test Case

Input

{
    "pdb_code": "1AKE",
    "ligand_smiles": "CC(=O)Oc1ccccc1C(=O)O"
}

Expected Steps

1. Download protein structure
2. Predict binding pockets
3. Prepare receptor for docking
4. Perform docking

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",
    "server-3": "https://scp.intern-ai.org.cn/api/v1/mcp/3/DrugSDA-Model"
}

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)
        sessions["server-3"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/3/DrugSDA-Model", stack)

        # Execute workflow steps
        # Step 1: Download protein 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: Predict binding pockets
        result_2 = await sessions["server-3"].call_tool("run_fpocket", arguments={})
        data_2 = parse(result_2)
        print(f"Step 2 result: {json.dumps(data_2, indent=2, ensure_ascii=False)[:500]}")

        # Step 3: Prepare receptor for docking
        result_3 = await sessions["server-2"].call_tool("convert_pdb_to_pdbqt_dock", arguments={})
        data_3 = parse(result_3)
        print(f"Step 3 result: {json.dumps(data_3, indent=2, ensure_ascii=False)[:500]}")

        # Step 4: Perform docking
        result_4 = await sessions["server-3"].call_tool("quick_molecule_docking", arguments={})
        data_4 = parse(result_4)
        print(f"Step 4 result: {json.dumps(data_4, indent=2, ensure_ascii=False)[:500]}")

        # Cleanup
        print("Workflow complete!")

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