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Coarse-grained models can be of great help to address the problem ofstructure prediction in nucleic acids. On one hand they can make the predictionmore efficient, while on the other hand, they can also help to identify theessential degrees of freedom and interactions for the description of a numberof structures. With the aim to provide an all-atom representation in anexplicit solvent to the predictions of our SPlit and conQueR (SPQR)coarse-grained model of RNA, we recently introduced a backmapping procedurewhich enforces the predicted structure into an atomistic one by means ofsteered Molecular Dynamics. These simulations minimize the ERMSD, a particularmetric which deals exclusively with the relative arrangement of nucleobases,between the atomistic representation and the target structure. In this paper,we explore the effects of this approach on the resulting interaction networksand backbone conformations by applying it on a set of fragments using as atarget their native structure. We find that the geometry of the targetstructures can be reliably recovered, with limitations in the regions withunpaired bases such as bulges. In addition, we observe that the folding pathwaycan also change depending on the parameters used in the definition of the ERMSDand the use of other metrics such as the RMSD.

Effects and limitations of a nucleobase-driven backmapping procedure for nucleic acids using steered Molecular Dynamics