Conformational Analysis of Oligosaccharides and Polysaccharides Using Molecular Dynamics Simulations

  • Martin Frank
Part of the Methods in Molecular Biology book series (MIMB, volume 1273)


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).

Key words

Molecular dynamics simulation Conformational analysis Conformational maps Carbohydrates Polysaccharides Hydrogen bonds 


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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Biognos ABGöteborgSweden

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