Unofficial PubChem MCP Server

MIT License

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substructure_search

Query PubChem database to identify compounds that contain a specified chemical substructure using SMILES notation, with customizable result limits.

Instructions

Find compounds containing a specific substructure

Input Schema

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

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 substructure query",
      "type": "string"
    }
  },
  "required": [
    "smiles"
  ],
  "type": "object"
}

Install Server

HTTP connection URL

Related Tools

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