Adapting molecular docking to study sialylated glycans
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Sialic acids are some of the most important molecules of life because they often occupy the terminal position in glycans attached to proteins and lipids on cell membranes, and are involved in many biological and pathological recognition phenomena. These interactions are difficult to study experimentally, hence, prediction of the geometry and binding affinity of sialic acid-protein interactions is of great significance. Molecular docking algorithms aiming to be applicable to a broad range of ligands suffer reduced accuracy when applied to carbohydrates since they are unable to incorporate ligand-specific conformational energies. This thesis reports the development of a set Carbohydrate Intrinsic (CHI) energy functions that quantify the conformational properties of sialic acid linkages (Neu5Acα-2-3Gal and Neu5Acα-2-6Gal) in glycans, and incorporates these functions into the docking software AutoDock Vina.