RNA junctions are secondary-structure elements formed when three or more helices come together. They are present in diverse RNA molecules with various fundamental functions in the cell. To better understand the intricate architecture of three-dimensional (3D) RNAs, we analyze currently solved 3D RNA junctions in terms of base-pair interactions and 3D configurations. First, we study base-pair in...

Oxygen greatly affects the mechanical properties of titanium. In addition, dislocations and twin boundaries influence the plastics deformation of hexagonal close-packed metals. As part of a systematic study of defects interactions in Ti, we investigate the interactions of oxygen with ð10 12Þ twin boundaries and ð10 10Þ prism plane stacking faults. The energetics of four interstitial sites in th...

The high level of conservation in ATP-binding sites of protein kinases increasingly demandsthe quest to find selective inhibitors with little cross reactivity. Kinase kinases are a recently discovered group of Kinases found to be involved in several mitotic events. These proteins represent attractive targets for cancer therapy with several small molecule inhibitors undergoing different ph...

The electrostatic model, which is widely used to explain π-involved interactions, gives an intuitive picture of these intermolecular interactions and has successfully predicted many phenomena in recent decades. Still, this simple model faces problems in certain cases and it has come under fire in previous studies on π-π stacking interactions. Here, employing ab initio calculations, we have iden...

In building and refining nucleic acid structures, it is often desirable to enforce particular base pairing and/or base stacking interactions. Energy-based modeling programs with classical molecular mechanics force fields do not lend themselves to the easy imposition of penalty terms corresponding to such restraints, because the requirement that two bases lie in or near the same plane (pairing) ...