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Methods Mol Biol. 2015;1273:359-77. doi: 10.1007/978-1-4939-2343-4_22.

Conformational analysis of oligosaccharides and polysaccharides using molecular dynamics simulations.

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Biognos AB, Generatorsgatan 1, 41705, Göteborg, Sweden,


Complex carbohydrates usually have a large number of rotatable bonds and consequently a large number of theoretically possible conformations can be generated (combinatorial explosion). The application of systematic search methods for conformational analysis of carbohydrates is therefore limited to disaccharides and trisaccharides in a routine analysis. An alternative approach is to use Monte-Carlo methods or (high-temperature) molecular dynamics (MD) simulations to explore the conformational space of complex carbohydrates. This chapter describes how to use MD simulation data to perform a conformational analysis (conformational maps, hydrogen bonds) of oligosaccharides and how to build realistic 3D structures of large polysaccharides using Conformational Analysis Tools (CAT).

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