Software for predicting the 3D structure of RNA molecules

Abstract

RNA is not regarded anymore as a simple transfer molecule between DNA and proteins. Indeed, over the past decades a plethora of new functional roles have been assigned to RNA molecules. Such functions are carried out either by RNA molecules alone or through interactions with DNA, other RNA molecules, or proteins. In all cases, the structure that the RNA molecule adopts will impact its function, as it happens with proteins. Therefore, to fully characterize the function of an RNA molecule, its structure needs to be either determined by experiments or predicted by computation. Unfortunately, our knowledge of the atomic mechanism by which RNA molecules adopt their biological active structures is still limited. Such hurdle is now being addressed by the development of new computational methods for RNA structure prediction, which complement experimental methods such as X-ray crystallography, nuclear magnetic resonance, small-angle X-ray scattering, and cryo-electron microscopy. This software focus is not dedicated to a single computational method but aims at outlining the most adopted methods for computational RNA structure prediction.