RNA 3D structure modeling by fragment assembly with small-angle X-ray scattering restraints.

IF 4.4 3区生物学 Q1 BIOCHEMICAL RESEARCH METHODS

Bioinformatics Pub Date : 2023-09-02 DOI:10.1093/bioinformatics/btad527

Grzegorz Chojnowski, Rafał Zaborowski, Marcin Magnus, Sunandan Mukherjee, Janusz M Bujnicki

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引用次数: 0

Abstract

Summary: Structure determination is a key step in the functional characterization of many non-coding RNA molecules. High-resolution RNA 3D structure determination efforts, however, are not keeping up with the pace of discovery of new non-coding RNA sequences. This increases the importance of computational approaches and low-resolution experimental data, such as from the small-angle X-ray scattering experiments. We present RNA Masonry, a computer program and a web service for a fully automated modeling of RNA 3D structures. It assemblies RNA fragments into geometrically plausible models that meet user-provided secondary structure constraints, restraints on tertiary contacts, and small-angle X-ray scattering data. We illustrate the method description with detailed benchmarks and its application to structural studies of viral RNAs with SAXS restraints.

Availability and implementation: The program web server is available at http://iimcb.genesilico.pl/rnamasonry. The source code is available at https://gitlab.com/gchojnowski/rnamasonry.

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基于小角度x射线散射约束的RNA片段组装三维结构建模。

摘要:结构测定是许多非编码RNA分子功能表征的关键步骤。然而，高分辨率RNA 3D结构测定的努力并没有跟上发现新的非编码RNA序列的步伐。这增加了计算方法和低分辨率实验数据的重要性，例如来自小角度x射线散射实验的数据。我们提出了RNA砌体，一个计算机程序和一个网络服务，用于RNA 3D结构的全自动建模。它将RNA片段组装成几何上合理的模型，以满足用户提供的二级结构约束、三级接触约束和小角度x射线散射数据。我们用详细的基准说明了方法描述，并将其应用于具有SAXS约束的病毒rna的结构研究。可用性和实现:程序web服务器可在http://iimcb.genesilico.pl/rnamasonry上获得。源代码可从https://gitlab.com/gchojnowski/rnamasonry获得。

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

Bioinformatics 生物-生化研究方法

CiteScore

11.20

自引率

5.20%

发文量

753

审稿时长

2.1 months

期刊介绍： The leading journal in its field, Bioinformatics publishes the highest quality scientific papers and review articles of interest to academic and industrial researchers. Its main focus is on new developments in genome bioinformatics and computational biology. Two distinct sections within the journal - Discovery Notes and Application Notes- focus on shorter papers; the former reporting biologically interesting discoveries using computational methods, the latter exploring the applications used for experiments.