Perception pharmacophore

The search for structural fragments (substructures) is very important in medicinal chemistry, QSAR, spectroscopy, and many other fields in the process of perception of pharmacophore, chromophore, or other -phores. 

Flexible 3D alignment of a set of ligands binding to the same target and/or CoMFA analysis allowing the perception of a pharmacophore for this target. 

Guner O F (Editor) 2000. Pharmacophore Perception, Development, and Use in Drug Design. International University Line Biotechnology Series, 2. 

Guner OF. Preface. In Guner OF, editor, Pharmacophore perception, development, and use in drug design. La Jolla International University Line, 2000. 

Clement, O.O. and Mehl, A.T. (2000) HipHop pharmacophores based on multiple common-feature alignments, in Pharmacophore Perception, Development, and Use in Drug Design (ed. O.F. Giiner), International University Line, La Jolla, CA, pp.69-84. 

Guner, O.E. Pharmacophore Perception, Use and Development in Drug Design, lUL Biotechnologies Series, USA, 2000. 

Giiner, O. F. and Henry, D. R. (2000) Metric for analyzing hit lists and pharmacophores. In Pharmacophore perception, development and use in drug design, Giiner, O. (ed.), International University Line, La Jolla, CA, pp.193-212... 

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]. 

This review is based on literature data and on the personal experience of the authors and should not represent a direct comparison between packages but rather a snapshot of the current developments in pharmacophore perception technology from our perspective. 

In order to have an objective view of the different available pharmacophore perception software tools, we chose to analyze these using the following criteria whenever possible ... 

Pharmacophore generation engine which type of pharmacophore perception engine is implemented in the program ... 

The currently available pharmacophore perception methods are reviewed here... 

Here, we consider it appropriate to mention briefly the so-called shape-based methods for flexible compound searching. Although these are not strictly seen in any relationship with the functional pharmacophore perception, the shape and size of compounds obviously influence activity and, in some cases, may be the main factors determining biological action. 

A lot of effort has been invested over the past 20 years in the optimization of the different steps of pharmacophore generation molecular editing and 3D representation, combinatorial enumeration, conformational expansion and pharmacophore perception methodologies for small drug-like data sets. However, we note that today there are still some areas with potential for improvement in the field of ligand-based pharmacophore modeling ... 

Guner OF (2000) Pharmacophore, Perception, Development and Use in Drug Design. University International line, San Diego, CA. 

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