Triplets of pharmacophoric points

Triplets of Pharmacophoric Point descriptors (or TOPP descriptors) encode information on presence/absence or occurrence frequencies of 3-point pharmacophores derived from molecular interaction fields (MlFs) [Sciabola, Morao et al., 2007 Lamanna, Catalano et al, 2007]. 

Some research groups have extended the atom-pair descriptors to three-point (triplets) and four-point (quartets) pharmacophore descriptors (35,37,76,81) as described in section 2. These descriptors have a potentially superior descriptive power, and a perceived advantage over atom pairs is the increased "shape" information (intrapharmacophore distance relationships) content of the individual descriptors (37a). The quartet (tetrahedral) four-point descriptors offer further potential 3D content by including information on volume and chirality (37a, 82), compared with the triplets that are components of the quartets and represent planes or "slices" through the 3D shapes. 

Triangular descriptors (or triplet descriptors) describe the relative positions of three atoms, group centroids, pharmacophore points, or surface points in the molecule [Pepperrell and... 

Then, queries are generated covering all possible triplets of PPP types and geometrical interatomic distances (i.e., 5916 geometrically valid queries) and used to search the molecules in the analyzed data set. To account for conformational flexibility of molecules, a tolerance is associated with each point-point distance. Finally, the molecular descriptor is obtained as a bit string indicating the queries (i.e., pharmacophores) hit by the compound. For each pharmacophore, it is possible to identify not only if a compound or database of compounds can express it, but also how many times it can express. 

PDT fingerprints (or Pharmacophore Definition Triplets fingerprints) are 3-point pharmacophore vectorial descriptors, where each bit is set to one or zero, depending on the presence or absence of a specific combination of three pharmacophoric points and three geometric distances [Matter and Potter, 1999]. 

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