PubChem MCP Server

MIT License

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search_similar_compounds

Identify chemically similar compounds using Tanimoto similarity. Input a SMILES string, set a similarity threshold, and retrieve relevant results from PubChem’s extensive chemical database.

Instructions

Find chemically similar compounds using Tanimoto similarity

Input Schema

Name	Required	Description
`max_records`	No	Maximum number of results (1-10000, default: 100)
`smiles`	Yes	SMILES string of the query molecule
`threshold`	No	Similarity threshold (0-100, default: 90)

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 molecule",
      "type": "string"
    },
    "threshold": {
      "description": "Similarity threshold (0-100, default: 90)",
      "maximum": 100,
      "minimum": 0,
      "type": "number"
    }
  },
  "required": [
    "smiles"
  ],
  "type": "object"
}

MCP directory API

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