核糖中心-适体：一个整合的，以结构为中心的RNA适体数据库。

IF 13.1 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Nucleic Acids Research Pub Date : 2025-10-21 DOI:10.1093/nar/gkaf1016

Zhizhong Lu,Hao Sun,Bo Fu,Ying Ao,Jiali Wang,Ke Chen,Yuhang Luo,Linfei Li,Zhaoji Qiu,Jiaxin Zhao,Yuxuan Sun,Zhijie Tan,Qiaozhen Liu,Yangyi Ren,Ziyu Guo,Xiaoxue Chen,Yuanlin He,Yingying Zhao,Yixin Chen,Mengxiao Li,Xuemei Peng,Baowei Huang,Shuang Zhu,Lin Huang,Zhichao Miao

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引用次数: 0

摘要

RNA适体作为“化学抗体”，具有与多种配体结合的优势，在诊断、治疗和生物传感方面具有变革性的应用。尽管有这些潜在的和现有的数据库，但由于缺乏将实验确定的结构数据与配体结合机制相结合的综合资源，合理的适体设计受到阻碍。在这里，我们提出了ribocenter -aptamer (https://aptamer.ribocentre.org/)，这是一个人工整理的数据库，用于捕获RNA适体结合的分子机制。我们的资源系统地在669篇出版物中编目了191种适体类型，统一了510个序列，123个小分子配体和344个蛋白质配体，并通过实验解决了二级/三级结构，配体结合袋，亲和力指标和功能注释。ribocenter -aptamer旨在将分子机制发现与转化工程相结合，为推进适体科学提供不可或缺的平台。

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Ribocentre-aptamer: an integrative, structure-focused database for RNA aptamers.

RNA aptamers function as 'chemical antibodies' with advantages in binding to diverse ligands, enabling transformative applications in diagnostics, therapeutics, and biosensing. Despite these potential and existing databases, rational aptamer design is hindered by the lack of integrated resources coupling experimentally determined structural data with ligand-binding mechanisms. Here, we present Ribocentre-aptamer (https://aptamer.ribocentre.org/), a manually curated database to capture the molecular mechanism of RNA aptamer binding. Our resource systematically catalogues 191 aptamer types across 669 publications, unifying 510 sequences, 123 small-molecule ligands, and 344 protein ligands with experimentally resolved secondary/tertiary structures, ligand-binding pockets, affinity metrics, and functional annotations. Ribocentre-aptamer aims to bridge molecular mechanism discovery with translational engineering, providing an indispensable platform for advancing aptamer science.

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来源期刊

Nucleic Acids Research 生物-生化与分子生物学

CiteScore

27.10

自引率

4.70%

发文量

1057

审稿时长

2 months

期刊介绍： Nucleic Acids Research (NAR) is a scientific journal that publishes research on various aspects of nucleic acids and proteins involved in nucleic acid metabolism and interactions. It covers areas such as chemistry and synthetic biology, computational biology, gene regulation, chromatin and epigenetics, genome integrity, repair and replication, genomics, molecular biology, nucleic acid enzymes, RNA, and structural biology. The journal also includes a Survey and Summary section for brief reviews. Additionally, each year, the first issue is dedicated to biological databases, and an issue in July focuses on web-based software resources for the biological community. Nucleic Acids Research is indexed by several services including Abstracts on Hygiene and Communicable Diseases, Animal Breeding Abstracts, Agricultural Engineering Abstracts, Agbiotech News and Information, BIOSIS Previews, CAB Abstracts, and EMBASE.