Pharmacophore screening

One of the most prominent reasons for the retrieval of false-positives in pharmacophore screens is the lack of spatial restriction of the models the chances that a compound will have the required features somewhere present in its structure increases with its size and flexibility. Therefore, most 3D pharmacophore methods have the possibility to add either inclusion or shape volumes that must be filled by the ligands, or forbidden or excluded volumes that describe the space that is occupied by atoms forming the binding site. 

Physicochemical properties of molecules Biological activity of drugs, including toxicity Search for pharmacophore Screening of combinatorial libraries Search of large databases Molecular similarity Molecular diversity Drug design... 

For those molecules with matching formula key, compare each pharmacophore screen key with the corresponding key of the database molecule using a logical AND. A nonzero result indicates that the keys have at least one bit in common, and so the screen criterion is satisfied. 

Sanders MPA, Barbosa AJM, Zaizycka B, Nicolaes GAP, Klomp JPG, de Vlieg J, Del Rio A (2012) Comparative analysis of pharmacophore screening tools. J Chem Inf Model 52 1607-1620... 

Tanrikulu Y, Rau O, Schwarz O et al (2009) Structure-based pharmacophore screening for natural-product-derived PPARgamma agonists. Chembiochem 10 75-78. doi 10.1002/... 

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