Pharmacophore Model Service of Pharmacophore Method in Docking Simulation

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.

Our services

Several options for combining docking-based virtual screening with pharmacodynamic-based virtual screening are available

• Before using docking simulation to evaluate, you can use pharmacophore search to pre-filter the ligand database.
• You can use the pharmacophore search to post-process the docking simulation results, and remove unbound compounds based on the pharmacophore search.
• Another alternative is to use pharmacophores for calibration during the docking simulation. The pharmacophore model can be used to elucidate the binding position of the ligand in this case.

In addition to the above services, we can also provide

• Ligand-based pharmacophore modeling

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.

• Receptor-based pharmacophore modeling

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.

• Pharmacophore model service without protein structure and without ligand structure

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.

• Pharmacophore model service with known protein and ligand structure

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.

• Pharmacophore Model Service without Protein Structure and without Ligand Structure
• Ligand-based Pharmacophore Model Service
• Pharmacophore Model Service with Known Protein and Ligand Structure
• Receptor-based Pharmacophore Model Service