Pharmacophoric alignment technique

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]. 

A widely used 3-D QSAR method that makes use of PLS is comparative molecular field analysis (CoMFA), in which a probe atom is used to calculate the steric and electronic fields at numerous points in a 3D lattice within which the molecules have been aligned. Poso et al. [56] used the technique to model the binding of coumarins to cytochrome P450 2A5, with similar results to those obtained by Bravi and Wikel [55]. Shi et al. [57] used it to model the estrogen receptor binding of a large diverse set of compounds, and Cavalli et al. [58] used it to develop a pharmacophore for hERG potassium... 

Current Super-positioning Techniques for Aligning 3D Pharmacophores and Molecules... 

The concepts of receptor and pharmacophore play a basic role in the alignment of molecules in - grid-based QSAR techniques. 

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