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internscience/scp/alanine-scanning-pipeline

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PublishedJune 16, 2026 at 11:17 PM

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version: "1.0.0" 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

Design alanine scan mutants
Compute parameters for mutants
Predict interactions for mutants
Compare protein properties

Test Case

Input

json

{
    "sequence": "MKTIIALSYIFCLVFA"
}

Expected Steps

Design alanine scan mutants
Compute parameters for mutants
Predict interactions for mutants
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.

python

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)
async def main():
    # Connect to required servers
    sessions = {}
    sessions["server-28"], _, _ = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/28/InternAgent", "sse")
    sessions["server-29"], _, _ = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/29/SciToolAgent-Bio", "sse")
    sessions["server-2"], _, _ = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool", "streamable-http")
    # Execute workflow steps
    # Step 1: Design alanine scan mutants
    result_1 = await sessions["server-28"].call_tool("AlanineScanningDesigner", arguments={})
    data_1 = parse(result_1)
    print(f"Step 1 result: {json.dumps(data_1, indent=2, ensure_ascii=False)[:500]}")
    # Step 2: Compute parameters for mutants
    result_2 = await sessions["server-29"].call_tool("ComputeProtPara", arguments={})
    data_2 = parse(result_2)
    print(f"Step 2 result: {json.dumps(data_2, indent=2, ensure_ascii=False)[:500]}")
    # Step 3: Predict interactions for mutants
    result_3 = await sessions["server-29"].call_tool("PredictDrugTargetInteraction", arguments={})
    data_3 = parse(result_3)
    print(f"Step 3 result: {json.dumps(data_3, indent=2, ensure_ascii=False)[:500]}")
    # Step 4: Compare protein properties
    result_4 = await sessions["server-2"].call_tool("calculate_protein_sequence_properties", 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())

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