Unofficial PubChem MCP Server

MIT License

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superstructure_search

Search for larger chemical compounds containing a specific query structure using SMILES input. Retrieve relevant results from over 110 million PubChem compounds for research and analysis.

Instructions

Find larger compounds that contain the query structure

Input Schema

Name	Required	Description	Default
`max_records`	No	Maximum number of results (1-10000, default: 100)
`smiles`	Yes	SMILES string of the query structure

Input Schema (JSON Schema)

{
  "properties": {
    "max_records": {
      "description": "Maximum number of results (1-10000, default: 100)",
      "maximum": 10000,
      "minimum": 1,
      "type": "number"
    },
    "smiles": {
      "description": "SMILES string of the query structure",
      "type": "string"
    }
  },
  "required": [
    "smiles"
  ],
  "type": "object"
}

Install Server

HTTP connection URL

Related Tools

superstructure_search
@Augmented-Nature/PubChem-MCP-Server
substructure_search
@Augmented-Nature/PubChem-MCP-Server
substructure_search
@Augmented-Nature/Augmented-Nature-PubChem-MCP-Server
search_by_smiles
@Augmented-Nature/PubChem-MCP-Server
search_by_smiles
@Augmented-Nature/Augmented-Nature-PubChem-MCP-Server
substructure_search
@Augmented-Nature/ChEMBL-MCP-Server

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