Three-dimensional fingerprints, molecular

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]. 

Listing 1 Examples of descriptor sets of the drug molecule diclofenac, a) Molecular fingerprints [21]. b) Substructure descriptors [22]. c) Autocorrelation coefficients, based on the three-dimensional interaction potential of the molecule [23]. 

Schuffenhauer A, Gillet VJ, Willett P. Similarity searching in files of three-dimensional chemical structures analysis of the BIOSTER database using two-dimensional fingerprints and molecular field descriptors. J Chem Inf Comput Sci 2000 40 295-307. 

Vibrational spectroscopy is one of the most important and crucial experimental tools broadly applied in chemistry, physics, and biology. Vibratitmal spectroscopy is unique in the sense that it provides a relationship between the three-dimensional organization of molecular stractures and their vibrational fingerprints. This book provides a snapshot of the tremendous developments that have been made in the field of gas phase spectroscopy for the structural characterization of (bio)-molecules and assemblies of molecules within the past decade. A preceding snapshot was given in the book by Schermann [1], Vibrational action spectroscopy has in particular experienced an amazingly successful era, with many new experimental developments and applications in many different areas in chemistry, analytical chemistry, physics, and biology. Previous reviews include [2-6], and updated reviews can be found in the present book. 

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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