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shape-similarity

separate

Performs 3D shape-based similarity searching using ROCS (OpenEye), USRCAT (ultra-fast), Open3DAlign (RDKit), ESPSim (electrostatic), and ShaEP with explicit handling of Tanimoto-Combo (shape + color), shape vs ECFP4 complementarity, conformer-ensemble searching, alignment optimization, and scaffold hopping. Use when searching for shape-mimicking compounds with different scaffolds, identifying bioisosteric replacements, prospective scaffold hopping, or expanding hit series beyond 2D similarity.

When to use

• 3D shape-based similarity searching
• searching for shape-mimicking compounds
• identifying bioisosteric replacements
• prospective scaffold hopping
• expanding hit series beyond 2D similarity
• Tanimoto-Combo scoring
• conformer-ensemble searching
• alignment optimization

When not to use

• 2D fingerprint similarity
• pharmacophore search with discrete feature constraints
• 3D conformer generation

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