PatSnap Chemical Molecular
About
PatSnap Chemical Molecular MCP is a Model Context Protocol server that equips AI agents with chemical intelligence capabilities, covering compound structure search, fragment analysis, and ADMET property prediction. Built on PatSnap's global life sciences platform, it accelerates
Details
- Transport
- SSE
Explore
- Compound structure search
- Fragment analysis
- ADMET property prediction
Setting up with Highlight
This MCP is not yet compatible with Highlight’s one-click setup. However, you can still use it with Highlight by following these steps:
- Download and install Highlight from highlightai.com/download
- Navigate to the plugins tab and select "Add Custom Plugin"
-
Configure the plugin with the settings below
Plugin Name
PatSnap Chemical MolecularCommand (node, npx, python, etc.)Please refer to the README for specific instructions on how to obtain API keys or other required environment variables.
- Enable "Start Automatically" if you want the plugin to start when Highlight launches
From the repository
``json``
{
"mcpServers": {
"patsnap-chemical-molecular": {
"url": "https://connect.patsnap.com/713886/logic-mcp?apikey=YOUR_API_KEY",
"type": "streamableHttp"
}
}
}
ls_structure_search
Search chemical structures. Use this tool when the user wants to search compounds by chemical structure. The Python service only keeps the MCP request parameters and forwards the payload to the downstream chemical endpoint. Args: smiles: str, query structure in SMILES format, example "CC(=O)OC1=C(C=CC=C1)C(O)=O" type: str, search type, supports "EXT" and "SIM" include_multi_component: bool, whether to include multi-component compounds, valid for EXT type only, default true i…
ls_structure_fetch
Fetch chemical structure details in batch. Batch fetch full detail records by InChIKey. Args: inchi_keys: List[str]. InChIKey list used to fetch compound details. Maximum 100 identifiers per request. Returns: dict[str, Any]: Response body: { "items": [ { "inchi_key": "BSYNRYMUTXBXSQ-UHFFFAOYSA-N", "compound_name": "ASPIRIN", "molecular_formula": "C9H8O4", "canonical_smiles": "CC(=O)Oc1ccccc1…
ls_patent_structure_fetch
Fetch patent-related chemical structures. Batch fetch chemical structures associated with a patent by patent ID or patent number. Args: patent_id: str, patent ID used to fetch related structures. pn: str, patent number used to resolve patent ID before fetching structures. offset: int, pagination offset, starting from 0. limit: int, page size. Maximum 100. Returns: dict[str, Any]: Response body: { "total": 28, "items": [ { …
ls_admet_predict
Predict ADMET properties for a list of molecules. Use this tool when the user wants to evaluate drug-likeness or pharmacokinetic properties of small molecules. It calls the ADMET-AI model to predict absorption, distribution, metabolism, excretion, and toxicity properties for each input SMILES. Args: smiles: List[str]. List of SMILES molecular formula strings. Each element must be a valid SMILES string (e.g. "CC(=O)Oc1ccccc1C(=O)O"). Minimum 1, maximum 100 molecules per r…
ls_chemical_mcs_analyze
Analyze fragment composition from multiple chemical structures. Use this tool when the user wants to analyze fragment distribution from a set of SMILES structures. It analyzes the frequent fragments and count how many times each fragment appears across the input structures. Args: structures: List[str]. List of SMILES structures to analyze. Must contain at least one valid SMILES string (e.g. ["CCO", "CC(C)O", "c1ccccc1"]). Returns: Dict[str, Any]: MCS analysis response. Sche…
Claude Desktop / Cursor
Paste into your MCP client config file to install this server.
{
"mcpServers": {
"patsnap chemical molecular": {
"patsnap-chemical-molecular": {
"url": "https://connect.patsnap.com/713886/logic-mcp?apikey=YOUR_API_KEY",
"type": "streamableHttp"
}
}
}
}McpServers
{
"patsnap-chemical-molecular": {
"url": "https://connect.patsnap.com/713886/logic-mcp?apikey=YOUR_API_KEY",
"type": "streamableHttp"
}
}Server Config
``json
{
"mcpServers": {
"patsnap-chemical-molecular": {
"url": "https://connect.patsnap.com/713886/logic-mcp?apikey=YOUR_API_KEY",
"type": "streamableHttp"
}
}
}
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