title: Conformational analysis of oligosaccharides and polysaccharides using molecular dynamics simulations.
abstract: 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).
authors.affiliation: Biognos AB, Generatorsgatan 1, 41705, Göteborg, Sweden, martin@glycosciences.org.
authors.forename: Martin
authors.initials: M
authors.lastname: Frank
mesh_terms: D002236:Carbohydrate Conformation; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D009844:Oligosaccharides / Q000737:chemistry*; D011134:Polysaccharides / Q000737:chemistry*; D012984:Software
chemical_list: D009844:Oligosaccharides; D011134:Polysaccharides