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Keywords = RNA pocket geometric feature

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19 pages, 7199 KiB  
Review
Advances and Mechanisms of RNA–Ligand Interaction Predictions
by Chen Zhuo, Chengwei Zeng, Haoquan Liu, Huiwen Wang, Yunhui Peng and Yunjie Zhao
Life 2025, 15(1), 104; https://doi.org/10.3390/life15010104 - 15 Jan 2025
Cited by 2 | Viewed by 1658
Abstract
The diversity and complexity of RNA include sequence, secondary structure, and tertiary structure characteristics. These elements are crucial for RNA’s specific recognition of other molecules. With advancements in biotechnology, RNA–ligand structures allow researchers to utilize experimental data to uncover the mechanisms of complex [...] Read more.
The diversity and complexity of RNA include sequence, secondary structure, and tertiary structure characteristics. These elements are crucial for RNA’s specific recognition of other molecules. With advancements in biotechnology, RNA–ligand structures allow researchers to utilize experimental data to uncover the mechanisms of complex interactions. However, determining the structures of these complexes experimentally can be technically challenging and often results in low-resolution data. Many machine learning computational approaches have recently emerged to learn multiscale-level RNA features to predict the interactions. Predicting interactions remains an unexplored area. Therefore, studying RNA–ligand interactions is essential for understanding biological processes. In this review, we analyze the interaction characteristics of RNA–ligand complexes by examining RNA’s sequence, secondary structure, and tertiary structure. Our goal is to clarify how RNA specifically recognizes ligands. Additionally, we systematically discuss advancements in computational methods for predicting interactions and to guide future research directions. We aim to inspire the creation of more reliable RNA–ligand interaction prediction tools. Full article
(This article belongs to the Section Genetics and Genomics)
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