--- name: virtual-screening-1afb4dfa591b description: "Virtual Screening Pipeline - Virtual screening: search PubChem by substructure, compute similarity, filter by drug-likeness, and predict binding affinity. Use this skill for drug discovery tasks involving search pubchem by smiles calculate smiles similarity calculate mol drug chemistry boltz binding affinity. Combines 4 tools from 3 SCP server(s)." --- # Virtual Screening Pipeline **Discipline**: Drug Discovery | **Tools Used**: 4 | **Servers**: 3 ## Description Virtual screening: search PubChem by substructure, compute similarity, filter by drug-likeness, and predict binding affinity. ## Tools Used - **`search_pubchem_by_smiles`** from `pubchem-server` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/8/Origene-PubChem` - **`calculate_smiles_similarity`** from `server-2` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool` - **`calculate_mol_drug_chemistry`** from `server-2` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool` - **`boltz_binding_affinity`** from `server-3` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/3/DrugSDA-Model` ## Workflow 1. Search similar compounds in PubChem 2. Compute molecular similarity 3. Filter by drug-likeness 4. Predict binding affinity ## Test Case ### Input ```json { "query_smiles": "c1ccc(-c2ccccc2)cc1", "target_protein": "MKTIIALSYIFCLVFA" } ``` ### Expected Steps 1. Search similar compounds in PubChem 2. Compute molecular similarity 3. Filter by drug-likeness 4. Predict binding affinity ## 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](https://scphub.intern-ai.org.cn). ```python 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 = { "pubchem-server": "https://scp.intern-ai.org.cn/api/v1/mcp/8/Origene-PubChem", "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, 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["pubchem-server"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/8/Origene-PubChem", stack) sessions["server-2"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool", stack) sessions["server-3"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/3/DrugSDA-Model", stack) # Execute workflow steps # Step 1: Search similar compounds in PubChem result_1 = await sessions["pubchem-server"].call_tool("search_pubchem_by_smiles", arguments={}) data_1 = parse(result_1) print(f"Step 1 result: {json.dumps(data_1, indent=2, ensure_ascii=False)[:500]}") # Step 2: Compute molecular similarity result_2 = await sessions["server-2"].call_tool("calculate_smiles_similarity", arguments={}) data_2 = parse(result_2) print(f"Step 2 result: {json.dumps(data_2, indent=2, ensure_ascii=False)[:500]}") # Step 3: Filter by drug-likeness result_3 = await sessions["server-2"].call_tool("calculate_mol_drug_chemistry", arguments={}) data_3 = parse(result_3) print(f"Step 3 result: {json.dumps(data_3, indent=2, ensure_ascii=False)[:500]}") # Step 4: Predict binding affinity result_4 = await sessions["server-3"].call_tool("boltz_binding_affinity", 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()) ``` --- Source attribution: SpectrAI-Initiative Original project: https://github.com/SpectrAI-Initiative/InnoClaw License: MIT License information: https://opensource.org/license/mit Original upstream instructions; downloaded from Dave AI. ## Upstream license notice MIT License Copyright (c) 2026 Gabriel Moreira Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. # Dave AI resource metadata Creator / publisher: SpectrAI-Initiative Original project: https://github.com/SpectrAI-Initiative/InnoClaw Attribution basis: Upstream repository explicitly recorded in package mirror path Fields of work: Data & Analytics, Education & Research, Healthcare & Life Sciences Roles: Clinical Research, Data Scientist, Researcher Specialties: API Tools: Pubchem Server, Server 2, Server 3 Country applicability: Country not specified Classification basis: Source catalog labels Instruction SHA-256: 9c7814fe41d796671448c82c5715be62d3bcf38166e0459a956aa7e56e4830be