RNAproDB：用于分析蛋白质-RNA相互作用的网络服务器和交互式数据库。

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

作者信息

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

机构信息

Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.

Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA.

出版信息

J Mol Biol. 2025 Feb 15:169012. doi: 10.1016/j.jmb.2025.169012.

DOI:10.1016/j.jmb.2025.169012

PMID:40126909

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.

摘要

我们展示了RNAproDB（https://rnaprodb.usc.edu/），这是一个全新的网络服务器、分析流程、数据库以及高度交互式的可视化工具，专为蛋白质-RNA复合物设计，适用于所有含核酸结构的形式。RNAproDB计算多种映射方案来放置核酸成分并恰当地呈现蛋白质-RNA相互作用。计算了各种结构注释，包括非经典碱基配对几何结构、氢键以及蛋白质-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。子图选择便于研究界面的较小组成部分。分子表面静电势可以可视化。RNAproDB能够分析和探索实验测定的、预测的以及设计的蛋白质-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。