RNA molecules play fundamental roles in cellular processes. Their function and interactions with other biomolecules are dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is laborious and challenging, and therefore, the majority of known RNAs remain structurally uncharacterized. Here, we present SimRNA: a new method for computational RNA 3D structure prediction, which uses a coarse-grained representation, relies on the Monte Carlo method for sampling the conformational space, and employs a statistical potential to approximate the energy and identify conformations that correspond to biologically relevant structures. SimRNA can fold RNA molecules using only sequence information, and, on established test sequences, it recapitulates secondary structure with high accuracy, including correct prediction of pseudoknots. For modeling of complex 3D structures, it can use additional restraints, derived from experimental or computational analyses, including information about secondary structure and/or long-range contacts. SimRNA also can be used to analyze conformational landscapes and identify potential alternative structures.

The dissociation energies from all rovibrational levels of H2 and D2 in the ground electronic state are calculated with high accuracy by including relativistic and quantum electrodynamics (QED) effects in the nonadiabatic treatment of the nuclear motion. For D2, the obtained energies have theoretical uncertainties of 0.001 cm(-1). For H2, similar uncertainties are for the lowest levels, while for the higher ones the uncertainty increases to 0.005 cm(-1). Very good agreement with recent high-resolution measurements of the rotational v = 0 levels of H2, including states with large angular momentum J, is achieved. This agreement would not have been possible without accurate evaluation of the relativistic and QED contributions and may be viewed as the first observation of the QED effects, mainly the electron self-energy, in a molecular spectrum. For several electric quadrupole transitions, we still observe certain disagreement with experimental results, which remains to be explained.

The dissociation energy of molecular hydrogen is determined theoretically with a careful estimation of error bars by including nonadiabatic, relativistic, and quantum electrodynamics (QED) corrections. The relativistic and QED corrections were obtained at the adiabatic level of theory by including all contributions of the order α 2 and α 3 as well as the major (one-loop) α 4 term, where α is the fine structure constant. The computed α 0 , α 2 , α 3 , and α 4 components of the dissociation energy of the H 2 isotopomer are 36118.7978 (2) 2

RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch aptamers and puzzle 7, a ribozyme structure, are included in this round of the experiment. The riboswitch structures include biological binding sites for small molecules (S-adenosyl methionine, cyclic diadenosine monophosphate, 5-amino 4-imidazole carboxamide riboside 5 ′ -triphosphate, glutamine) and proteins (YbxF), and one set describes large conformational changes between ligand-free and ligand-bound states. The Varkud satellite ribozyme is the most recently solved structure of a known large ribozyme. All puzzles have established biological functions and require structural understanding to appreciate their molecular mechanisms. Through the use of fast-track experimental data, including multidimensional chemical mapping, and accurate prediction of RNA secondary structure, a large portion of the contacts in 3D have been predicted correctly leading to similar topologies for the top ranking predictions. Template-based and homologyderived predictions could predict structures to particularly high accuracies. However, achieving biological insights from de novo prediction of RNA 3D structures still depends on the size and complexity of the RNA. Blind computational predictions of RNA structures already appear to provide useful structural information in many cases. Similar to the previous RNA-Puzzles Round II experiment, the prediction of non-Watson-Crick interactions and the observed high atomic clash scores reveal a notable need for an algorithm of improvement. All prediction models and assessment results are available at http://ahsoka.ustrasbg.fr/rnapuzzles/.