RNAproDB: A Webserver and Interactive Database for Analyzing Protein–RNA Interactions

IF 4.7 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Biology Pub Date : 2025-02-15 DOI:10.1016/j.jmb.2025.169012

Raktim Mitra , Ari S. Cohen , Wei Yu Tang , Hirad Hosseini , Yongchan Hong , Helen M. Berman , Remo Rohs

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引用次数: 0

Abstract

We present RNAproDB (https://rnaprodb.usc.edu/), a new webserver, analysis pipeline, database, and highly interactive visualization tool, designed for protein–RNA complexes, and applicable to all forms of nucleic acid containing structures. RNAproDB computes several mapping schemes to place nucleic acid components and present protein–RNA interactions appropriately. Various structural annotations are computed including non-canonical base-pairing geometries, hydrogen bonds, and protein–RNA and RNA–RNA water-mediated interactions. This information is presented through integrated visualization and data tools. Subgraph selection facilitates studying smaller components of the interface. Molecular surface electrostatic potential can be visualized. RNAproDB enables analyzing and exploring experimentally determined, predicted, and designed protein–nucleic acid complexes. We present a quantitative analysis of pre-analyzed protein–RNA structures in RNAproDB revealing statistical patterns of molecular binding and recognition.

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RNAproDB：一个分析蛋白质- rna相互作用的web服务器和交互式数据库。

我们提出了RNAproDB (https://rnaprodb.usc.edu/)，一个新的web服务器，分析管道，数据库和高度交互式可视化工具，设计用于蛋白质- rna复合物，并适用于所有形式的核酸含有结构。RNAproDB计算几种定位方案来放置核酸成分并适当地呈现蛋白质- rna相互作用。计算各种结构注释，包括非规范碱基配对几何，氢键，蛋白质- rna和RNA-RNA水介导的相互作用。这些信息通过集成的可视化和数据工具呈现。子图选择便于研究接口的较小组成部分。分子表面静电势可以可视化。RNAproDB能够分析和探索实验确定，预测和设计的蛋白质核酸复合物。我们对RNAproDB中预先分析的蛋白质- rna结构进行了定量分析，揭示了分子结合和识别的统计模式。

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.