The pharmacophore model is very suitable as a search for a virtual screening database. However, more commonly used in virtual screening is the layered method, also known as the funnel principle, in which different methods are continuously combined, and the most likely compounds with poor activity are removed in each successive step. The layered method can be used to screen the most promising compounds. Equally useful, molecular docking simulation is a calculation method aimed at predicting the binding mode of a compound of a given receptor and the quality of interaction, usually by using a scoring function to predict affinity. Molecular docking simulation can be used to screen large databases of compounds and sort the compounds according to their predicted affinity.
|Pharmacophore Modeling Service in Docking Simulation
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In the absence of the macromolecular target structure, ligand-based pharmacophore modeling is an essential stratege for drug discovery. In this method, the common chemical characteristics from 3D structures of multiple known ligands are extracted through ligand alignment, which would represent the essential interactions between ligand and potential macromolecular target.
The structural information of protein receptors is known, but there is no active ligand. In this case, the putative pharmacophore model can be constructed by analyzing the chemical nature of the target binding site.
If the target structure and all its ligands are unknown, pharmacophore modeling is very difficult. In fact, 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.
Such structure-based pharmacophore queries have multiple applications: they can be used for virtual screening, ligand binding posture prediction, and comparison of binding sites.
CD ComputaBio offers a corresponding pharmacophore modeling service. Our Pharmacophore modeling service in docking simulation can provide accurate approximations of real molecular behaviors and have proven to be very useful in understanding the biochemical basis of physiological events at different stages of drug development, even in different fields such as materials science. Our team of experts can provide up to one millisecond of simulation time for the system you choose, so you do not have to worry about technical issues. We can also analyze these results for you. CD ComputaBio team has been working in this field for more than ten years and has published his findings in top scientific journals.