Deep dive into RNA: a systematic literature review on RNA structure prediction using machine learning methods

Abstract

Abstract The discovery of non-coding RNAs (ncRNAs) has expanded our comprehension of RNAs’ inherent nature and capabilities. The intricate three-dimensional structures assumed by RNAs dictate their specific functions and molecular interactions. However, the limited number of mapped structures, partly due to experimental constraints of methods such as nuclear magnetic resonance (NMR), highlights the importance of in silico prediction solutions. This is particularly crucial in potential applications in therapeutic drug discovery. In this context, machine learning (ML) methods have emerged as prominent candidates, having previously demonstrated prowess in solving complex challenges across various domains. This review focuses on analyzing the development of ML-based solutions for RNA structure prediction, specifically oriented toward recent advancements in the deep learning (DL) domain. A systematic analysis of 33 works reveals insights into the representation of RNA structures, secondary structure motifs, and tertiary interactions. The review highlights current trends in ML methods used for RNA structure prediction, demonstrates the growing research involvement in this field, and summarizes the most valuable findings.