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The computational modeling of RNA and its interactions is of crucial importance for the understanding of the wide variety of biological functions it performs. Among these approaches, several coarse-grained models employ structural databases to derive their energy functions or to define scoring functions for structure prediction purposes. In many cases, the parametrization is done by using as a reference a set of experimentally determined structures, or data obtained from Molecular Dynamics simulations. Since the two choices are clearly different, we present here a brief comparison of the essential spaces of a set of conformations of two topologically connected nucleotides generated by these means. We find that when the nucleotides are embedded into a duplex, the essential spaces of both ensembles are quite restricted and do not differ substantially. Nevertheless, when the conformational space of a free dinucleoside monophosphate simulation is compared against a similar set obtained from the structural database, the differences of the essential spaces are considerable. In addition, we show a brief comparison of a specific distance between the nucleotides which correlates with the sugar pucker of the first nucleotide, and analyze its distribution under similar conditions.
This article was published in the following journal.
Name: Journal of chemical information and modeling
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