Ligand-based screening searches for compounds that reproduce features of a reference ligand or an aligned set of ligands. Prepare a chemically correct 3D query and review its conformation and alignment before screening.

• Flexible APF screening aligns compounds from an SD database to the Atomic Property Fields of the reference ligand(s).
• RIDE searches a prepared conformer database for matching 3D shapes and atomic properties.
• Chemical superposition and APF tools help prepare and inspect the query.

For multiple reference ligands, use a consistent coordinate frame. Review the influence of individual atoms, envelope penalties, and any receptor excluded volume. APF similarity scores describe agreement with the query and should not be interpreted as receptor binding energies.

If a suitable receptor structure is available, selected hits can be followed up with receptor-based docking. Inspect retained query features, chemical diversity, and receptor compatibility before selecting compounds for testing.