The pharmacophore model contains multiple functions of a specific 3D model. Each feature is usually represented as a sphere (despite changes), and the radius determines the deviation tolerance from the precise position. These functions can be marked as a single function or any logical combination of "AND," "OR," and "NOT." If a molecule can be placed in a sphere that represents the query feature, the molecule is considered a hit molecule. In general, pharmacodynamic group queries may be too complicated to find hit molecules from a given library. In this case, only certain functions that are considered essential to the activity can be matched. Adjusting molecules or facilitating molecular docking simulations are other uses of the model. Depending on the situation and the type of experiment, a variety of strategies can be used to manually build a pharmacophore model, or an automatic algorithm can be used.
Figure 1. Pharmacophore model.
|Project Name||Pharmacophore Model Construction Service|
|Samples requirement||Our pharmacophore model construction service requires you to provide specific drug construction requirements.|
|Timeline||Decide according to your needs.|
|Deliverables||We provide you with raw data and calculation result analysis service.|
||If the target structure and all its ligands are unknown, pharmacophore modeling is very difficult. Considering the large number of available protein structures and potential compound formulas is to better model pharmacophores in order to effectively cover the chemical space in any search process.|
||If only a single active molecule is known, the only option may be to use similarity queries (for example, using pharmacophore fingerprints) to retrieve similar molecules.|
||Such structure-based pharmacophore queries have multiple applications: they can be used for virtual screening, ligand binding posture prediction, and comparison of binding sites.|
||The structural information of protein receptors is known, but there is no active ligand. In this case, a putative pharmacophore model can be constructed by analyzing the chemical properties of the binding site of interest.|
The pharmacophore model is mainly used in three areas:
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