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pharmacophore-modeling

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Builds and applies 3D pharmacophore models using RDKit Pharm3D, the apo2ph4 receptor-based workflow (Heider et al. 2023), Pharmer / Pharmit for search, and PharmacoForge for protein-pocket-conditioned pharmacophore generation (Flynn et al. 2025), covering ligand-based pharmacophores from active-set alignment and receptor-based pharmacophores from binding-pocket geometry. Explicitly handles feature types, geometric tolerances, partial matching, and pharmacophore-based virtual screening. Use when identifying scaffold-hopping candidates, building shape-and-feature search queries, or transferring SAR across chemotypes.

When to use

• identifying scaffold-hopping candidates
• building shape-and-feature search queries
• transferring SAR across chemotypes
• ligand-based pharmacophores from active-set alignment
• receptor-based pharmacophores from binding-pocket geometry
• pharmacophore-based virtual screening
• generating pocket-conditioned pharmacophores

When not to use

• 2D scaffold-based searches
• 3D shape similarity
• protein-ligand interaction analysis

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