| name | patsnap-chemical-molecular |
| description | Patsnap Chemical Molecular MCP for AI agents. Search 160M+ chemical structures, synthetic routes, and bioactivity data via specialized chemistry tools. |
| homepage | https://open.patsnap.com/marketplace/mcp-servers/chemical-molecular |
| metadata | {"author":"Patsnap","category":"Life Science","version":"1.0.0","requires":{"mcp_endpoint":"https://connect.patsnap.com/713886/logic-mcp?apikey=YOUR_API_KEY"}} |
Setup
Get your API Key at https://open.patsnap.com
Patsnap Chemical Molecular
This skill connects your AI agent to Patsnap's Chemical Molecular MCP server — providing professional-grade chemistry search and analysis capabilities.
With this skill, your agent can navigate the complex world of small molecules, from structure-based patent searching to bioactivity data retrieval and synthetic route analysis.
Prerequisites
This skill requires the Patsnap Chemical Intelligence MCP server to be configured in your environment:
{
"mcpServers": {
"chemical_molecular": {
"url": "https://connect.patsnap.com/713886/logic-mcp?apikey=YOUR_API_KEY",
"type": "streamableHttp"
}
}
}
Get your API key at open.patsnap.com.
For the full list of available tools and input parameters, refer to the official MCP server documentation:
https://open.patsnap.com/marketplace/mcp-servers/chemical-molecular
Instructions for AI Agents
Step 1: Chemical Entity Recognition
When a user mentions a chemical name, drug, or SMILES string, use the chemical normalization tools to resolve the entity to a standard structure or Patsnap internal ID.
Step 2: Structure-Based Search
- Use Substructure Search to find molecules containing a specific scaffold.
- Use Similarity Search to find analogs of a lead compound.
- Combine structure search with patent filters to investigate the chemical IP landscape.
Step 3: Bioactivity & Property Analysis
Retrieve IC50, Ki, and other bioactivity data from literature and patents to evaluate compound potency and selectivity.
Step 4: Output Synthesis
Present chemical data with:
- SMILES/InChI strings for precise identification.
- Visual descriptions of scaffolds and functional groups.
- Tabular comparisons of bioactivity across different analogs.
Example Workflows
Lead Optimization Support
- Identify lead compound structure.
- Run similarity search to find known analogs.
- Retrieve bioactivity data for all analogs to identify SAR (Structure-Activity Relationship) trends.
Chemical IP Clearance
- Input a candidate molecule structure.
- Run substructure search across global patent databases.
- Identify key patents that may cover the candidate scaffold.
Resources
