State-of-the-RNArt: benchmarking current methods for RNA 3D structure prediction

Abstract

RNAs are essential molecules involved in numerous biological functions. Understanding RNA functions requires the knowledge of their 3D structures. Computational methods have been developed for over two decades to predict the 3D conformations from RNA sequences. These computational methods have been widely used and are usually categorised as eitherab initioor template-based. The performances remain to be improved. Recently, the rise of deep learning has changed the sight of novel approaches. Deep learning methods are promising, but the adaptation to RNA 3D structure prediction remains at stake. In this work, we give a brief review of theab initio, template-based and novel deep learning approaches. We highlight the different available tools and provide a benchmark on nine approaches using the RNA-Puzzles dataset. We provide an online dashboard that shows the predictions made by benchmarked models, freely available on the EvryRNA platform:https://evryrna.ibisc.univ-evry.fr.