alanine-scanning-pipeline

name	alanine_scanning_pipeline
description	Alanine Scanning Mutagenesis Pipeline - Alanine scanning: design scan, compute properties for each mutant, predict interactions, and compare. Use this skill for protein biochemistry tasks involving AlanineScanningDesigner ComputeProtPara PredictDrugTargetInteraction calculate protein sequence properties. Combines 4 tools from 3 SCP server(s).

Alanine Scanning Mutagenesis Pipeline

Discipline: Protein Biochemistry | Tools Used: 4 | Servers: 3

Description

Alanine scanning: design scan, compute properties for each mutant, predict interactions, and compare.

Tools Used

• AlanineScanningDesigner from server-28 (sse) - https://scp.intern-ai.org.cn/api/v1/mcp/28/InternAgent
• ComputeProtPara from server-29 (sse) - https://scp.intern-ai.org.cn/api/v1/mcp/29/SciToolAgent-Bio
• PredictDrugTargetInteraction from server-29 (sse) - https://scp.intern-ai.org.cn/api/v1/mcp/29/SciToolAgent-Bio
• calculate_protein_sequence_properties from server-2 (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool

Workflow

1. Design alanine scan mutants
2. Compute parameters for mutants
3. Predict interactions for mutants
4. Compare protein properties

Test Case

Input

{
    "sequence": "MKTIIALSYIFCLVFA"
}

Expected Steps

1. Design alanine scan mutants
2. Compute parameters for mutants
3. Predict interactions for mutants
4. Compare protein properties

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-28": "https://scp.intern-ai.org.cn/api/v1/mcp/28/InternAgent",
    "server-29": "https://scp.intern-ai.org.cn/api/v1/mcp/29/SciToolAgent-Bio",
    "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)

  ():
    
    sessions = {}
    sessions[], _, _ =  connect(, )
    sessions[], _, _ =  connect(, )
    sessions[], _, _ =  connect(, )

    
    
    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())