PubChem structure and similarity search

Structure-based search lets you query PubChem by SMILES, InChIKey, or CID for exact matches, substructure motifs, or Tanimoto-ranked similar compounds. For similarity search the threshold most affects the result: start near 90 for close analogs and lower toward 60-70 to broaden the search.

PubChem structure and similarity search

Use structure-based queries when you have SMILES, InChIKey, or a CID. You run them by asking Ivy in chat, for example "Find PubChem compounds at least 80% similar to gefitinib".

Exact search

• Provide canonical SMILES or InChIKey for the most precise match.
• Use exact when you need a single canonical record (CID).

Substructure search

• Give Ivy a substructure SMILES or SMARTS pattern; the search runs PubChem's fingerprint-based substructure screening (fastsubstructure).
• Useful for scaffold exploration; expect broader result sets than exact.
• Returns 20 compounds by default; ask for up to 50.

Similarity search

• Give Ivy a compound name, SMILES, or CID plus a similarity threshold.
• The threshold is an integer 0-100 (not a 0.0-1.0 Tanimoto fraction) — minimum 50, default 90.
• Start at 90 for close analogs; lower toward 60-70 for broader exploration.
• Higher thresholds yield fewer, more similar hits. Returns 20 compounds by default; ask for up to 100.

Tips

• Normalize salts/charges before submission to avoid duplicated hits.
• Capture the threshold and search mode in logs so exports stay reproducible.
• If results seem empty, retry with similarity search at a lower threshold.