Molecular simulations of carbohydrates and protein–carbohydrate interactions: motivation, issues and prospects
Woods, Robert J.
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Fadda, Elisa; Woods, Robert J. (2010). Molecular simulations of carbohydrates and protein–carbohydrate interactions: motivation, issues and prospects. Drug Discovery Today 15 (15), 596-609
The characterization of the 3D structure of oligosaccharides, their conjugates and analogs is particularly challenging for traditional experimental methods. Molecular simulation methods provide a basis for interpreting sparse experimental data and for independently predicting conformational and dynamic properties of glycans. Here, we summarize and analyze the issues associated with modeling carbohydrates, with a detailed discussion of four of the most recently developed carbohydrate force fields, reviewed in terms of applicability to natural glycans, carbohydrate-protein complexes and the emerging area of glycomimetic drugs. In addition, we discuss prospectives and new applications of carbohydrate modeling in drug discovery.