Triplet descriptors

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

Good et al. 3 have extended the use of simple ligand triplet descriptors to encompass molecular surface comparisons and have made it possible to store... 

C, E E Hodgkin and Richards W G 1993. The Utilisation of Gaussian Functions for the Rapid nation of Molecular Similarity. Journal of Chemical Information and Computer Science 32 188-192. C and I D Kuntz 1995, Investigating the Extension of Pairwise Distance Pharmacophore sures to Triplet-based Descriptors, Journal of Computer-Aided Molecular Design 9 373-379. 

Good, A.G. and Kuntz, I.D. Investigating the extension of pairwise distance pharmacophore measures to triplet-based descriptors./. Comput.-Aided Mol. Des. 1995, 9, 373-379. 

The three components of the triplet are vectorially added to the corresponding entries of the atom-descriptor. However, this addition is subject to the limitation, that the resulting vector may not contain any negative elements. 

Beyond similarity-based applications, machine learning techniques may pick the specific descriptor elements that appear to correlate with the observed activity trends throughout a training set. Unlike in overlay models, where there is an obvious link between pharmacophore spheres or fields in space and their source atoms, the actual pairs (triplets, etc) of atoms in molecules that incarnate the picked descriptor elements must be first established, to gain any potential insights into the binding mechanisms. 

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. 

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