Protein complementary pharmacophore

The multiple potential pharmacophores for targets, such as protein active sites, are defined using complementary site points to exposed features accessible in the site. These site points (see section 2.3) create a hypothetical molecule that interacts with all pharmacophoric regions of the site. Figure 2 illustrates site points that were used for the thrombin site in selectivity studies for three serine protease inhibitors (see section 4.3). The potential pharmacophores are calculated for this molecule just as for any... 

Proteins can also be compared, with or without using information from ligands that bind to them. From the protein site points FLAP identifies the pharmacophores that are in common on-the-fly. Then complementarities between the proteins are evaluated maximizing the site-point features and the shape complementary between protein cavities. The resultant matches are then written out to a file. 

Figure 5.8. Example of privileged four-point pharmaeophores, either ereated from a ligand using a particular feature (e.g., the centroid of a "privileged" substructure) or complementary to a protein site using a site point or attachment point of a docked scaffold. Only pharmacophores that include this special feature are included in the fingerprint, thus providing a relative measure of diversity 1 similarity with respect to the privileged feature.

Complementary groups on the protein target recognize key features of the ligand. The three-dimensional arrangement of these features is commonly referred to as a pharmacophore. The Medicinal Chemistry Section of lUPAC has published a glossary of terms used in medicinal chemistry that includes an entry for the concept pharmacophore or pharmacophoric pattern. ... 

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