International Institute of Molecular and Cell Biology, Warsaw 02-109, Poland.
European Molecular Biology Laboratory, Hamburg Unit, Hamburg 22607, Germany.
Bioinformatics. 2023 Sep 2;39(9). doi: 10.1093/bioinformatics/btad527.
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.
The program web server is available at http://iimcb.genesilico.pl/rnamasonry. The source code is available at https://gitlab.com/gchojnowski/rnamasonry.
结构确定是非编码 RNA 分子功能特性研究的关键步骤。然而，高分辨率 RNA 三维结构的确定速度赶不上新非编码 RNA 序列的发现速度。这增加了计算方法和低分辨率实验数据（如小角度 X 射线散射实验）的重要性。我们提出了 RNA Masonry，这是一个计算机程序和一个网络服务，用于全自动构建 RNA 三维结构。它将 RNA 片段组装成符合用户提供的二级结构约束、三级接触约束和小角度 X 射线散射数据的几何上合理的模型。我们通过详细的基准测试来说明方法描述，并将其应用于具有 SAXS 约束的病毒 RNA 的结构研究。
该程序的网络服务器可在 http://iimcb.genesilico.pl/rnamasonry 上获得。源代码可在 https://gitlab.com/gchojnowski/rnamasonry 上获得。
