Interaction with a ligand molecule is very important for many proteins to carry out their biological function. This interaction is usually specific, not only in terms of the protein molecules involved in the interaction, but also in the location (i.e., the ligand binding site) in which this interaction happens. There are two popular models of how legends fit to their specific substrate: the induced fit model and the lock and key model. Residues in the binding site interact with the ligand by forming hydrogen bonds, hydrophobic interactions, or temporary van der Waals interactions to make a protein-ligand complex. Protein ligand binding site prediction can help us to well understand the binding mechanism between the ligand and protein molecule, and so aid drug discovery. Now, bioinformaticians at Creative Proteomics are proud to tell you we are open to help you with Protein Ligand Binding Site Prediction Service!
In order to gain knowledge about the interaction, the protein molecule’s function and how to influence its activity by, for example, designing small molecule drugs, great efforts have been made to develop approaches that can predict ligand binding sites (LBSs) of proteins computationally, and a large number of ligand computational biology tools are now available for LBS prediction. In general, due to the location specificity of LBSs, the majority of these methods have exploited one or more of four types of properties (geometric, energetic, statistical, and evolutionary) in order to distinguish the ligand binding site from other parts of the protein surface.
According to the basis of the site-distinguishing properties, methods for predicting protein ligand binding site provided by Creative Proteomics can be classified into the following categories:
- Template-based: those that make use of homologous or similar structures with already known binding sites
- Geometry-based: those that carry out some kind of geometric computation to identify binding site pockets
- Energy-based: those that compute the interaction energy using imaginary ligands as binding probes
- Propensity-based: those that compute the propensity of a certain property that indicates a statistically significant preference for known LBSs, rather than non-LBSs
- Combination-based and others: those that perform the prediction based on the results of other methods and those that cannot be easily classified into one of the above categories
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As one of the leading omics industry company in the world! Creative Proteomics now is opening to provide protein ligand binding site prediction service for our customers. With over 8 years experience in the field of bioinformatics, we are willing to provide the most outstanding service to our customer! Contact us for all the detailed information!