Comparing RNA Kissing Interactions at Single-Molecule and Ensemble Levels

William Stephenson, Papa Nii Asare-Okai, Scott Tenenbaum, Daniele Fabris, Pan T.X. Li
2014 Biophysical Journal  
From a number of crystallographic structures of high molecular weight RNA molecules, we derived a set of effective potentials that describe the interactions between nucleotide centroids. Using this information, we developed a new Force Field that was implemented in a Molecular Dynamics code whose objective is to describe the three-dimensional folding of RNA molecules. The acceptance criterion for the resulting structures from MD simulations is through the minimum potential energy. Our simulated
more » ... structures were compared to experimental NMR results and we found a good structural similarity measured by the RMSD.
doi:10.1016/j.bpj.2013.11.1659 fatcat:vupm2yfx6nharltrfe33hbhoy4