Three-dimensional pharmacophore fingerprints

Xue L, Stahura FL, Godden JW, Bajorath J. Mini-fingerprints detect similar activity of receptor ligands previously recognized only by three-dimensional pharmacophore-based methods. J Chem Inf Comp Sci 2001 41 394-401. 

Often, all alignment-based methods and molecular field and potential calculations are classified as pharmacophore perception techniques. We will include most of these methods in this review however, when using the term pharmacophore model, we will be referring mainly to one specific type of perception, namely three-dimensional feature-based pharmacophore models represented by geometry or location constraints, qualitative or quantitative. An extrapolation of the pharmacophore approach to a set of multi-dimensional descriptors (pharmacophore fingerprints) has been developed mostly for library design and focusing purposes [3-8]. 

Multipoint pharmacophore fingerprints have also been used to compare libraries. For example, Pickett et al. [17] have represented libraries by the union of the individual molecular fingerprints and were able to identify regions of multipoint pharmacophore space that were not covered or that were underrepresented. McGregor and Muskal [37,38] developed a similar approach that is based on a low-dimensional pharmacophore space obtained by applying principal components analysis to the three-point pharmacophore representations of the compounds. 

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