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similarity-searching

separate

Performs molecular similarity searching using Tanimoto, Tversky, Dice, and cosine coefficients on bit/count fingerprints with explicit choice rules for symmetric vs asymmetric measures, scaffold-hopping vs lead-optimization regimes, activity-cliff diagnosis, and large-library nearest-neighbor methods (BulkTanimoto, MHFP6 LSH forest, USRCAT). Use when ranking compounds by structural resemblance to a query, clustering libraries, finding analogs, or diagnosing activity cliffs.

When to use

• | Scenario | Coefficient | Why | |----------|-------------|-----| | Standard analog search (drug-like, ECFP4) | Tanimoto, start near 0.7 | Repository starting heuristic; calibrate against project actives and analog judgments | | Sensitive…

When not to use

• 3D shape similarity
• molecular descriptor generation

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