ZINCPharmer is free  pharmacophore  search software for screening the purchasable subset of the ZINC  database (updates occur monthly). ZINCPharmer can import LigandScout and MOE pharmacophore definitions, as well as identify pharmacophore features directly from structure.
From PDB structure

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Targeting a protein-protein interaction? Design a pharmacophore from the PPI with PocketQuery.
Interactive Examples
Teach-Discover-Treat: DHODH (PDB)
As part of the Teach-Discover-Treat competition, this pharmacophore for the anti-malarial target dihydroorotate dehydrogenase was developed during an interactive exercise. Compounds matching this pharmacophore were ranked using smina energy minimization and the top compounds were tested in an inhibition assay. The tested compounds had a 27% hit rate in the primary assay.
Glycolytic Enzymes (PDB)
Protozoan parasites such as Plasmodium falciparum, a malarial agent, often lack a functional tricarboxylic cycle and so depend upon glycotic pathways for energy. As a result, inhibitors of these pathways are potential drug candidates. A pharmacophore for the inhibitory interaction of PDB 1M7O was derived using LigandScount. ZincPharmer successfully retrieves the original ligand (ZINC3869933) as well as several analogs.
Kinase Inhibitors (PDB)
Kinase inhibitors are often used in the treatment of cancer and inflammation. ZincPharmer's automatic pharmacophore feature detection was applied to the inhibitor of PDB 3K5U and important features were manually selected. The resulting screen identifies ZINC02425758, which is annotated as a potential tyrosine protein kinase inhibitor.

The ZincPharmer search technology uses the Pharmer open source pharmacophore search technology to efficiently search a large database of fixed conformers for pharmacophore matches. The search performance scales with the complexity and breadth of the pharmacophore query. Most searches take less than a minute. Please feel free to provide feedback in the forum.

Citation: If you find ZINCPharmer useful, please cite our Nucleic Acids Research paper.
This open access technology is funded through R01GM097082 and R01GM108340 from the National Institute of General Medical Sciences. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute of General Medical Sciences or the National Institutes of Health.