Molecular simulations of carbohydrates and protein-carbohydrate interactions: motivation, issues and prospects

Fadda, Elisa and Woods, Robert J. (2010) Molecular simulations of carbohydrates and protein-carbohydrate interactions: motivation, issues and prospects. Drug Discovery Today, 15 (15-16), 596-609. (doi:10.1016/j.drudis.2010.06.001).

Record type: Review

Abstract

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. The current state of carbohydrate force fields is reviewed with a focus on developmental differences and applicability in the growing area of glycomimetic design. © 2010 Elsevier Ltd.

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