mutation-impact-analysis

# 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 ```json { "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 `<YOUR_SCP_HUB_API_KEY>` with your own SCP Hub API Key. You can obtain one from the [SCP Platform](https://scphub.intern-ai.org.cn). ```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-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, 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-3"], _, _ = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/3/DrugSDA-Model", "streamable-http") sessions["server-1"], _, _ = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/1/VenusFactory", "sse") sessions["ensembl-server"], _, _ = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl", "streamable-http") # 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()) ```