A structure based design approach by definition is centered on the knowledge of the target protein structure. In absence of availability of such a structure a computationally generated model of the target based on a homologous protein is commonly used. Docking of the candidate small molecule into the correct active site of the target is a required step in determining the binding of the molecule to its target. Computationally predicted binding is often the only way of practically predicting the binding of the molecule with the target in-vitro or in-vivo.
VLife’s Protein Modeling and Docking service can assist in performing a complete structure base design project. Scope of these services could include optimizing the structure of the target protein, if available in public databases or developing a homology model of the target protein to replicate the target within very stringent levels of accuracy. This could be followed by an analysis of the protein or the model to identify active sites, mapping of the cavities and channels followed by docking of the small molecule into the correct cavity.
A choice of docking methods and techniques coupled with a variety of scoring functions enable our scientists to complete the design exercise in the most comprehensive manner. A specialized infrastructure combining the very best technologies for modeling, docking and visualization with a multi core parallel processing computational cluster enables our scientists to deliver this services in the most time efficient way.