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version: "1.0.1" name: enzyme_inhibitor_design description: "Enzyme Inhibitor Design - Design enzyme inhibitor: target structure, pocket prediction, compound screening, and ADMET assessment. Use this skill for enzyme pharmacology tasks involving retrieve protein data by pdbcode pred pocket prank quick molecule docking pred molecule admet calculate mol drug chemistry. Combines 5 tools from 2 SCP server(s)."
Enzyme Inhibitor Design
Discipline: Enzyme Pharmacology | Tools Used: 5 | Servers: 2
Description
Design enzyme inhibitor: target structure, pocket prediction, compound screening, and ADMET assessment.
Tools Used
- `retrieve_protein_data_by_pdbcode` from
server-2(streamable-http) -https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool - `pred_pocket_prank` from
server-3(streamable-http) -https://scp.intern-ai.org.cn/api/v1/mcp/3/DrugSDA-Model - `quick_molecule_docking` from
server-3(streamable-http) -https://scp.intern-ai.org.cn/api/v1/mcp/3/DrugSDA-Model - `pred_molecule_admet` from
server-3(streamable-http) -https://scp.intern-ai.org.cn/api/v1/mcp/3/DrugSDA-Model - `calculate_mol_drug_chemistry` from
server-2(streamable-http) -https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool
Workflow
- Get enzyme structure
- Predict active site pockets
- Dock inhibitor candidates
- Predict ADMET
- Check drug-likeness
Test Case
Input
json
{"pdb_code": "1AKE","ligand_smiles": "CC(=O)Oc1ccccc1C(=O)O"}
Expected Steps
- Get enzyme structure
- Predict active site pockets
- Dock inhibitor candidates
- Predict ADMET
- Check drug-likeness
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 asyncioimport jsonfrom mcp import ClientSessionfrom mcp.client.streamable_http import streamablehttp_clientfrom mcp.client.sse import sse_clientSERVERS = {"server-2": "https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool","server-3": "https://scp.intern-ai.org.cn/api/v1/mcp/3/DrugSDA-Model"}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, transportdef 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.textreturn str(result)except: return str(result)async def main():# Connect to required serverssessions = {}sessions["server-2"], _, _ = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool", "streamable-http")sessions["server-3"], _, _ = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/3/DrugSDA-Model", "streamable-http")# Execute workflow steps# Step 1: Get enzyme structureresult_1 = await sessions["server-2"].call_tool("retrieve_protein_data_by_pdbcode", arguments={})data_1 = parse(result_1)print(f"Step 1 result: {json.dumps(data_1, indent=2, ensure_ascii=False)[:500]}")# Step 2: Predict active site pocketsresult_2 = await sessions["server-3"].call_tool("pred_pocket_prank", arguments={})data_2 = parse(result_2)print(f"Step 2 result: {json.dumps(data_2, indent=2, ensure_ascii=False)[:500]}")# Step 3: Dock inhibitor candidatesresult_3 = await sessions["server-3"].call_tool("quick_molecule_docking", arguments={})data_3 = parse(result_3)print(f"Step 3 result: {json.dumps(data_3, indent=2, ensure_ascii=False)[:500]}")# Step 4: Predict ADMETresult_4 = await sessions["server-3"].call_tool("pred_molecule_admet", arguments={})data_4 = parse(result_4)print(f"Step 4 result: {json.dumps(data_4, indent=2, ensure_ascii=False)[:500]}")# Step 5: Check drug-likenessresult_5 = await sessions["server-2"].call_tool("calculate_mol_drug_chemistry", arguments={})data_5 = parse(result_5)print(f"Step 5 result: {json.dumps(data_5, indent=2, ensure_ascii=False)[:500]}")# Cleanupprint("Workflow complete!")if __name__ == "__main__":asyncio.run(main())