Computational prediction of RNA tertiary structures using machine learning methods

RNAs play crucial and versatile roles in biological processes. Computational prediction approaches can help to understand RNA structures and their stabilizing factors, thus providing information on their functions, and facilitating the design of new RNAs. Machine learning (ML) techniques have made tremendous progress in many fields in the past few years. Although their usage in protein-related fields has a long history, the use of ML methods in predicting RNA tertiary structures is new and rare. Here, we review the recent advances of using ML methods on RNA structure predictions and discuss the advantages and limitation, the difficulties and potentials of these approaches when applied in the field. Introduction RNAs are macromolecules of crucial and versatile biological functions. To fully understand their functions, knowledge of the three-dimensional (3D) structures is essential. Since experimental approaches to determinate RNA 3D structures are difficult and expensive, many computational approaches have been developed to this purpose. To date, although template-based and homology-modeling methods could achieve high accuracies, de novo predictions still depends on the size and complexity of the RNA, and further improvement in predicting non-canonical interactions are required, according to the recent RNA-Puzzles round III. For a comprehensive study of the recent work, we refer readers to the relevant literature.