Molecular Similarity (Tanimoto)
Compare two molecules and get their Tanimoto similarity using FP2, FP3, FP4 or MACCS fingerprints. A score of 1.0 means identical fingerprints, 0.0 means no overlap.
How Tanimoto similarity works
Each molecule is converted into a binary fingerprint — a bit string where each bit means "this substructure is present". The Tanimoto coefficient is the number of shared bits divided by the number of bits present in either molecule:
T = (A ∩ B) / (A ∪ B)
Rules of thumb widely used in cheminformatics: T > 0.85 usually means the same compound, T > 0.5 suggests a similar scaffold, and T < 0.3 indicates little structural overlap.
Which fingerprint should I use?
- FP2 — Daylight-style path-based fingerprint, good general-purpose choice.
- FP3 — smaller, faster, more permissive.
- FP4 — SMARTS-based, emphasises functional groups.
- MACCS — 166 predefined structural keys, very interpretable.