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mutation_impact_analysis

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Mutation Impact Analysis - Analyze mutation impact: predict structure, predict mutations from sequence and structure, and check variant effects with Ensembl VEP. Use this skill for molecular biology tasks involving pred protein structure esmfold zero shot sequence prediction predict zero shot structure get vep hgvs. Combines 4 tools from 3 SCP server(s).

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Mutation Impact Analysis

Discipline: Molecular Biology | Tools Used: 4 | Servers: 3

Description

Analyze mutation impact: predict structure, predict mutations from sequence and structure, and check variant effects with Ensembl VEP.

Tools Used

  • pred_protein_structure_esmfold from server-3 (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/3/DrugSDA-Model
  • zero_shot_sequence_prediction from server-1 (sse) - https://scp.intern-ai.org.cn/api/v1/mcp/1/VenusFactory
  • predict_zero_shot_structure from server-1 (sse) - https://scp.intern-ai.org.cn/api/v1/mcp/1/VenusFactory
  • get_vep_hgvs from ensembl-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl

Workflow

  1. Predict protein structure
  2. Predict mutations from sequence
  3. Predict mutations from structure
  4. Check variant effects with VEP

Test Case

Input

{
    "sequence": "MKTIIALSYIFCLVFA",
    "hgvs": "ENSP00000269305.4:p.Val600Glu"
}

Expected Steps

  1. Predict protein structure
  2. Predict mutations from sequence
  3. Predict mutations from structure
  4. Check variant effects with VEP

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-3": "https://scp.intern-ai.org.cn/api/v1/mcp/3/DrugSDA-Model",
    "server-1": "https://scp.intern-ai.org.cn/api/v1/mcp/1/VenusFactory",
    "ensembl-server": "https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl"
}

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-3"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/3/DrugSDA-Model", stack)
        sessions["server-1"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/1/VenusFactory", stack)
        sessions["ensembl-server"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl", stack)

        # Execute workflow steps
        # Step 1: Predict protein structure
        result_1 = await sessions["server-3"].call_tool("pred_protein_structure_esmfold", arguments={})
        data_1 = parse(result_1)
        print(f"Step 1 result: {json.dumps(data_1, indent=2, ensure_ascii=False)[:500]}")

        # Step 2: Predict mutations from sequence
        result_2 = await sessions["server-1"].call_tool("zero_shot_sequence_prediction", arguments={})
        data_2 = parse(result_2)
        print(f"Step 2 result: {json.dumps(data_2, indent=2, ensure_ascii=False)[:500]}")

        # Step 3: Predict mutations from structure
        result_3 = await sessions["server-1"].call_tool("predict_zero_shot_structure", arguments={})
        data_3 = parse(result_3)
        print(f"Step 3 result: {json.dumps(data_3, indent=2, ensure_ascii=False)[:500]}")

        # Step 4: Check variant effects with VEP
        result_4 = await sessions["ensembl-server"].call_tool("get_vep_hgvs", 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())