Profacgen, a biotechnology company that offers a broad service portfolio designed to provide versatile and reliable platforms for protein production and research, recently released protein-carbohydrate docking for its molecular docking service, offering unparalleled opportunities for drug discovery.
Carbohydrates participate in numerous important signaling pathways, and carbohydrate recognition is an essential component of many biological processes such as innate immunity, metabolism, and immune response. Glycans on cell surfaces, for example, or secreted biomolecules, play an important role in cell-cell interactions, including interactions between host cells and pathogens. Glycan-protein interactions are gaining importance in the field of structure-based drug design due to their physiological and pathological significance. However, because sugar moieties typically have a heterogeneous chemical structure and conformation, studying these interactions using X-ray crystallography has been notoriously difficult. Computational molecular modeling techniques provide an appealing alternative method for investigating protein-carbohydrate recognition and specificity.
At Profacgen, scientists predict these protein–carbohydrate interactions through the combination of a genetic conformational search algorithm coupled with an empirical free energy function specific for carbohydrates. Its docking procedure allows for a systematic exploration of carbohydrate ligand orientations and positions within a protein cavity (which is typically more open and less well-defined than small molecule binding sites) and assesses free energies of complex formation. Experiment-derived constraints can also be applied to the docking protocol to restrict the search space for the sugar as well as the protein molecule. The energy function is specifically designed for carbohydrates, which is used for the clustering of binding poses and exploration of the most energetically favorable complex structure.
“Our computational modeling method is well suited to provide an atomic-level understanding of carbohydrate recognition which reveals some of the distinctive molecular features unique to protein-carbohydrate complexes. We can also help to predict the interaction between proteins and single carbohydrate ligands and the binding poses and binding affinities of glycans to glycan-binding proteins.” Said Crystal, the chief marketing staff at Profacgen.
Visit our website to know more about the protein glycan docking service provided by Profacgen.