protein-engineering

name	protein_engineering
description	Protein Engineering Workflow - Engineer a protein: predict structure, identify functional residues, predict beneficial mutations, and calculate properties. Use this skill for protein engineering tasks involving Protein structure prediction ESMFold predict functional residue zero shot sequence prediction calculate protein sequence properties. Combines 4 tools from 2 SCP server(s).

Protein Engineering Workflow

Discipline: Protein Engineering | Tools Used: 4 | Servers: 2

Description

Engineer a protein: predict structure, identify functional residues, predict beneficial mutations, and calculate properties.

Tools Used

• Protein_structure_prediction_ESMFold from server-1 (sse) - https://scp.intern-ai.org.cn/api/v1/mcp/1/VenusFactory
• predict_functional_residue from server-1 (sse) - https://scp.intern-ai.org.cn/api/v1/mcp/1/VenusFactory
• zero_shot_sequence_prediction from server-1 (sse) - https://scp.intern-ai.org.cn/api/v1/mcp/1/VenusFactory
• calculate_protein_sequence_properties from server-2 (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool

Workflow

1. Predict 3D structure with ESMFold
2. Identify functional residues
3. Predict beneficial mutations
4. Calculate physicochemical properties

Test Case

Input

{
    "sequence": "MKTIIALSYIFCLVFAGKRDEFPSTWYV"
}

Expected Steps

1. Predict 3D structure with ESMFold
2. Identify functional residues
3. Predict beneficial mutations
4. Calculate physicochemical properties

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-1": "https://scp.intern-ai.org.cn/api/v1/mcp/1/VenusFactory",
    "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)

  ():
      AsyncExitStack()  stack:
        
        sessions = {}
        sessions[] =  connect(, stack)
        sessions[] =  connect(, stack)

        
        
        result_1 =  sessions[].call_tool(, arguments={})
        data_1 = parse(result_1)
        ()

        
        result_2 =  sessions[].call_tool(, arguments={})
        data_2 = parse(result_2)
        ()

        
        result_3 =  sessions[].call_tool(, arguments={})
        data_3 = parse(result_3)
        ()

        
        result_4 =  sessions[].call_tool(, arguments={})
        data_4 = parse(result_4)
        ()

        
        ()

 __name__ == :
    asyncio.run(main())