RNApdbee 3.0: A unified web server for comprehensive RNA secondary structure annotation from 3D coordinates.

IF 4.5 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Biology Pub Date : 2026-04-07 DOI:10.1016/j.jmb.2026.169795

Jan Pielesiak, Kamil Niznik, Pawel Snioszek, Gabriel Wachowski, Mikolaj Zurawski, Maciej Antczak, Marta Szachniuk, Tomasz Zok

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引用次数: 0

Abstract

RNApdbee 3.0 (publicly available at https://rnapdbee.cs.put.poznan.pl/) offers an advanced pipeline for comprehensive RNA structural annotation, integrating 2D and 3D data to build detailed nucleotide interaction networks. It classifies base pairs as canonical or noncanonical using the Leontis-Westhof and Saenger schemes and identifies stacking, base-ribose, base-phosphate, and base-triple interactions. The tool handles incomplete or modified residues, marking missing nucleotides and distinguishing noncanonical base pairs for accurate and effective visualization. Results are provided in standard formats - namely, extended dot-bracket notation, BPSEQ, and CT - and in detailed graphical visualizations. RNApdbee decomposes 2D structures into stems, loops, and single strands and offers flexible pseudoknot encoding. Its unified framework addresses inconsistencies across structural data formats by standardizing all inputs to PDBx/mmCIF and integrating seven widely used annotation tools. Finally, RNApdbee ensures reliable, format-independent, and comprehensive RNA structural annotation and interpretation.

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RNApdbee 3.0：一个统一的web服务器，用于从3D坐标进行全面的RNA二级结构注释。

RNApdbee 3.0（公开下载网址：// RNApdbee .cs.put.poznan.pl/）提供了一个先进的管道，用于全面的RNA结构注释，整合2D和3D数据来构建详细的核苷酸相互作用网络。它使用Leontis-Westhof和Saenger方案将碱基对分类为规范或非规范，并识别堆叠，碱基-核糖，碱基-磷酸盐和碱基三重相互作用。该工具处理不完整或修饰的残基，标记缺失的核苷酸和区分非规范碱基对，以实现准确有效的可视化。结果以标准格式（即扩展点括号表示法、BPSEQ和CT）和详细的图形可视化形式提供。RNApdbee将二维结构分解为茎、环和单链，并提供灵活的伪结编码。它的统一框架通过标准化PDBx/mmCIF的所有输入和集成七种广泛使用的注释工具，解决了结构数据格式之间的不一致性。最后，RNApdbee保证了可靠的、格式无关的、全面的RNA结构注释和解释。

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.