Quantitative structure-activity relationship (QSAR) is the "quantitative" establishment of the relationship between the chemical structure and biological activity of a given small molecule. Based on specific structural features or having atomic, group, or molecular properties, such as lipophilicity, polarizability, electronic and spatial properties, QSAR models can be used to predict the activity of new chemical substances, including the affinity of ligands to their binding sites, inhibition constants, rate constants, etc.
Our company provides professional 3D-QSAR services, which can effectively guide the synthesis of a series of compounds with a common skeleton, and the obtained results can be used to predict the activity of this series of compounds, and further guide the modification and optimization of the compounds.
Service Overview
Customers can effectively complete force field calculations that call for three-dimensional (3D) structures of training sets using Our company's 3D-QSAR service platform. Then feature extraction and subsequent machine learning techniques minimize the size of the newly formed data space.
Our process comprises the study of biological data, improvement of biomolecule 3D structures, identification of bioactive conformations, computation of molecular interaction energy fields, creation and validation of 3D QSAR models, etc.
This one-stop 3D-QSAR workflow is designed to help customers forecast the biological activity of untested compounds, discover the factors that influence small molecule biological activity, and improve the activity of current leads.
Research Capabilities
Data mining method
Molecular mining methods, a special case of structured data mining methods, apply similarity matrix-based predictions or schemes for automatic segmentation into molecular substructures. In addition, there exist methods using max-common graph searches or graph kernels.
Matched pair analysis
A typical QSAR model derived from nonlinear machine learning is viewed as a "black box" that cannot guide medicinal chemists. Recently, there is a relatively new concept of matched molecular pair analysis or prediction-driven MMPA, which is combined with QSAR models to identify activity cliffs.
Fig.1 3D-QSAR, pharmacophore, and molecular docking studies were performed on DAPY analogues that were synthesized. (Liu G, et al. 2018)
Structural Parameters
| Hydrophobicity parameter | The absorption and distribution process of a drug in the body is closely related to its hydrophobicity, so hydrophobicity is an important characteristic that affects the physiological activity of a drug. |
| Electrical parameters | The electrical parameters in the two-dimensional (2D) quantitative structure-activity relationship are used to characterize the effect of substituents on the overall electron distribution of the molecule, and their values are also additions of substituents. |
| Stereo parameters | Commonly used stereo parameters include Tafto stereo parameters, molar refractive index, van der Waals radius, etc. |
| Geometric parameters | Commonly used geometric parameters include molecular surface area, solvent-accessible surface area, molecular volume, multidimensional stereooscopic parameters, etc. |
| Topological parameters | Structural parameters are used in the molecular linkage method. Topological parameters encode each atom according to the topology of the molecule and use the resulting code to characterize the molecular structure. |
| Physical and chemical properties parameters | Dipole moments, molecular spectral data, frontier orbital energy levels, acid-base dissociation constants, and other physical and chemical properties are sometimes used as structural parameters to participate in quantitative structure-activity relationship studies. |
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Reference
- Liu G, et al. (2018). "Application of 3D-QSAR, Pharmacophore, and Molecular Docking in the Molecular Design of Diarylpyrimidine Derivatives as HIV-1 Nonnucleoside Reverse Transcriptase Inhibitors." Int. J. Mol. Sci. 19(5): 1436.
Related Services
It should be noted that our service is only used for research, not for clinical use.
