Three-dimensional structures of RNA obtained by means of knowledge-based interaction potentials. O. Taxilaga-Zetina, P. Pliego-Pastrana and M. D. Carbajal-Tinoco. ISSN: 1539-3755. DOI: 10.1103/PhysRevE.81.041914.
We derive a set of effective potentials describing the interaction between pairs of nucleotides that belong to an RNA molecule. Such interaction potentials are then used as the main constituents of a simplified simulation model, which is tested in the description of small secondary structure motifs. Our simulated RNA hairpins are consistent with the experimental structures obtained by NMR.