Advances in the field of RNA 3D structure prediction and modeling, with purely theoretical approaches, and with the use of experimental data

IF 4.4 2区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Structure Pub Date : 2024-09-24 DOI:10.1016/j.str.2024.08.015

Sunandan Mukherjee, S. Naeim Moafinejad, Nagendar Goud Badepally, Katarzyna Merdas, Janusz M. Bujnicki

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Abstract

Recent advancements in RNA three-dimensional (3D) structure prediction have provided significant insights into RNA biology, highlighting the essential role of RNA in cellular functions and its therapeutic potential. This review summarizes the latest developments in computational methods, particularly the incorporation of artificial intelligence and machine learning, which have improved the efficiency and accuracy of RNA structure predictions. We also discuss the integration of new experimental data types, including cryoelectron microscopy (cryo-EM) techniques and high-throughput sequencing, which have transformed RNA structure modeling. The combination of experimental advances with computational methods represents a significant leap in RNA structure determination. We review the outcomes of RNA-Puzzles and critical assessment of structure prediction (CASP) challenges, which assess the state of the field and limitations of existing methods. Future perspectives are discussed, focusing on the impact of RNA 3D structure prediction on understanding RNA mechanisms and its implications for drug discovery and RNA-targeted therapies, opening new avenues in molecular biology.

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利用纯理论方法和实验数据在 RNA 3D 结构预测和建模领域取得的进展

最近在 RNA 三维（3D）结构预测方面取得的进展为 RNA 生物学提供了重要见解，凸显了 RNA 在细胞功能中的重要作用及其治疗潜力。本综述总结了计算方法的最新发展，特别是人工智能和机器学习的应用，它们提高了 RNA 结构预测的效率和准确性。我们还讨论了新实验数据类型的整合，包括低温电子显微镜（cryo-EM）技术和高通量测序技术，它们改变了 RNA 结构建模。实验进展与计算方法的结合代表了 RNA 结构测定领域的重大飞跃。我们回顾了 RNA-Puzzles 和结构预测关键评估（CASP）挑战的成果，评估了该领域的现状和现有方法的局限性。我们还讨论了未来的前景，重点是 RNA 三维结构预测对理解 RNA 机制的影响及其对药物发现和 RNA 靶向疗法的影响，为分子生物学开辟了新的途径。

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来源期刊

Structure 生物-生化与分子生物学

CiteScore

8.90

自引率

1.80%

发文量

155

审稿时长

3-8 weeks

期刊介绍： Structure aims to publish papers of exceptional interest in the field of structural biology. The journal strives to be essential reading for structural biologists, as well as biologists and biochemists that are interested in macromolecular structure and function. Structure strongly encourages the submission of manuscripts that present structural and molecular insights into biological function and mechanism. Other reports that address fundamental questions in structural biology, such as structure-based examinations of protein evolution, folding, and/or design, will also be considered. We will consider the application of any method, experimental or computational, at high or low resolution, to conduct structural investigations, as long as the method is appropriate for the biological, functional, and mechanistic question(s) being addressed. Likewise, reports describing single-molecule analysis of biological mechanisms are welcome. In general, the editors encourage submission of experimental structural studies that are enriched by an analysis of structure-activity relationships and will not consider studies that solely report structural information unless the structure or analysis is of exceptional and broad interest. Studies reporting only homology models, de novo models, or molecular dynamics simulations are also discouraged unless the models are informed by or validated by novel experimental data; rationalization of a large body of existing experimental evidence and making testable predictions based on a model or simulation is often not considered sufficient.