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WIREs Comput Mol Sci
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Carbohydrate force fields

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Abstract Carbohydrates present a special set of challenges to the generation of force fields. First, the tertiary structures of monosaccharides are complex merely by virtue of their exceptionally high number of chiral centers. In addition, their electronic characteristics lead to molecular geometries and electrostatic landscapes that can be challenging to predict and model. The monosaccharide units can also interconnect in many ways, resulting in a large number of possible oligosaccharides and polysaccharides, both linear and branched. These larger structures contain a number of rotatable bonds, meaning they potentially sample an enormous conformational space. This article briefly reviews the history of carbohydrate force fields, examining and comparing their challenges, forms, philosophies, and development strategies. Then it presents a survey of recent uses of these force fields, noting trends, strengths, deficiencies, and possible directions for future expansion. © 2011 John Wiley & Sons, Ltd. This article is categorized under: Molecular and Statistical Mechanics > Molecular Mechanics

Fraction of reviewed force fields, per decade ending with 2010, employing quantum mechanical (QM) methodologies in the development of atomistic charges (blue) and torsion parameters (red). In the first decade, only two CarbFFs were published, and neither used any QM methods.

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Force field use by application class and force field category.

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There is a distinct lack of trend in carbohydrate force field treatment of the anomeric effect.

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Number of carbohydrate force fields, per decade, classified according to the number of energetic components in their functional form.

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Number of carbohydrate force fields, per decade, by classification.

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Number of carbohydrate force fields (CarbFFs), per decade, categorized by the overall system to which the design was targeted. Some CarbFFs (red) were designed to treat small subsets of carbohydrates by modeling only specific anomers, saccharides or linkages. Others were designed to treat a more general set of carbohydrates within a biological context (green) or as organic molecules (blue).

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Fraction of reviewed force fields, per decade, for which nuclear magnetic resonance [NMR (red)] and crystallographic data (blue) were used as experimental validation. The reversal of trends in the 1980s almost certainly reflects advances in computing and NMR.

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Molecular and Statistical Mechanics > Molecular Mechanics

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