A (critical) survey of modelling protocols used to explore the conformational space of oligosaccharides

Abstract Computational methods are intensively applied to explore the conformational space of oligosaccharides. In this report, the current modelling protocols for the conformational analysis of carbohydrates are reviewed. Approaches which need direct input of experimental data from NMR experiments (distance mapping and restrained molecular dynamics), various systematic search strategies (uniform rotation, relaxed and adiabatic maps) and random sampling techniques (random molecular mechanics calculations and Metropolis Monte Carlo simulations) are compared. Recently, molecular dynamics simulations have begun to play a dominant role for the conformational analysis of oligosaccharides. Therefore, various commonly used molecular dynamics simulation protocols (e.g. the use of different dielectric constants, simulated annealing and high-temperature simulation protocols, inclusion of explicit solvent molecules, the choice of appropriate non-bonded interaction cut-offs) which are increasingly used to obtain information about all the accessible conformations are discussed in detail.

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