KDBI-RP: Kinetic Data of RNA-Protein Interactions Database.

IF 4.5 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Biology Pub Date : 2025-11-01 Epub Date: 2025-07-25 DOI:10.1016/j.jmb.2025.169357

Yunpeng He, Dongyue Hou, Yuzong Chen, Xian Zeng

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引用次数: 0

Abstract

Biomolecular interaction kinetics underpin essential cellular mechanisms, yet quantitative databases remain scarce for RNA-protein interactions (RPIs)-a critical regulatory axis in post-transcriptional control, synthetic biology, and therapeutic development. We previously established KDBI (Kinetic Data of Bio-molecular Interactions database) to catalog quantitative kinetics data across diverse biomolecular interaction types. Here, we present KDBI-RP, a dedicated extension focused on RPI kinetics, addressing the growing demand for RNA-centric kinetic research. KDBI-RP systematically integrates binding data for RNA-protein interactions, including kinetic rate constants-association (k_on, 3657 entries) and dissociation (k_off, 3761 entries)-supplemented by equilibrium dissociation constants (K_d, 175,932 entries). The database offers well-curated information on kinetic constants, assay conditions, literature sources, and comprehensive sequence, structural, and functional annotations for proteins, RNAs, and their complexes. KDBI-RP is freely accessible at http://www.kdbirp.aiddlab.com. We anticipate that KDBI-RP will serve as a valuable resource for the RNA biology and RNA-based medicine research communities.

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KDBI-RP: rna -蛋白相互作用动力学数据数据库。

生物分子相互作用动力学是基本细胞机制的基础，然而rna -蛋白相互作用（rpi）的定量数据库仍然缺乏，rpi是转录后控制、合成生物学和治疗发展的关键调控轴。我们之前建立了KDBI（生物分子相互作用动力学数据数据库），对不同生物分子相互作用类型的定量动力学数据进行分类。在这里，我们提出了KDBI-RP，一个专注于RPI动力学的专用扩展，解决了以rna为中心的动力学研究日益增长的需求。KDBI-RP系统地整合了rna -蛋白质相互作用的结合数据，包括动力学速率常数-关联（kon, 3,657个条目）和解离（koff, 3,761个条目）-辅以平衡解离常数（Kd, 175,932个条目）。该数据库提供了动力学常数，分析条件，文献来源，以及蛋白质，rna及其复合物的综合序列，结构和功能注释的精心策划的信息。KDBI-RP可在http://www.kdbirp.aiddlab.com免费访问。我们期望KDBI-RP将成为RNA生物学和基于RNA的医学研究界的宝贵资源。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Journal of Molecular Biology 生物-生化与分子生物学

CiteScore

11.30

自引率

1.80%

发文量

412

审稿时长

28 days

期刊介绍： Journal of Molecular Biology (JMB) provides high quality, comprehensive and broad coverage in all areas of molecular biology. The journal publishes original scientific research papers that provide mechanistic and functional insights and report a significant advance to the field. The journal encourages the submission of multidisciplinary studies that use complementary experimental and computational approaches to address challenging biological questions. Research areas include but are not limited to: Biomolecular interactions, signaling networks, systems biology; Cell cycle, cell growth, cell differentiation; Cell death, autophagy; Cell signaling and regulation; Chemical biology; Computational biology, in combination with experimental studies; DNA replication, repair, and recombination; Development, regenerative biology, mechanistic and functional studies of stem cells; Epigenetics, chromatin structure and function; Gene expression; Membrane processes, cell surface proteins and cell-cell interactions; Methodological advances, both experimental and theoretical, including databases; Microbiology, virology, and interactions with the host or environment; Microbiota mechanistic and functional studies; Nuclear organization; Post-translational modifications, proteomics; Processing and function of biologically important macromolecules and complexes; Molecular basis of disease; RNA processing, structure and functions of non-coding RNAs, transcription; Sorting, spatiotemporal organization, trafficking; Structural biology; Synthetic biology; Translation, protein folding, chaperones, protein degradation and quality control.