patsnap-chemical-molecular

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

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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.

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Example Workflows

Lead Optimization Support

1. Identify lead compound structure.
2. Run similarity search to find known analogs.
3. Retrieve bioactivity data for all analogs to identify SAR (Structure-Activity Relationship) trends.