Deriving RNA topological structure from SAXS

Gallego, José; Wang, Yun-Xing

doi:10.1016/bs.mie.2022.08.037

Cited by 1 publication

(1 citation statement)

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“…Computational structure prediction methods offer an alternative to experimental structure determination, but the purely theoretical models are often of limited accuracy. One promising approach is the computational modeling with the use of restraints derived from low-resolution experimental data ( Bernetti et al 2021 , Mazzanti et al 2021 , Fang et al 2022 ). To address this issue, we developed RNA Masonry, a computer program for fully automated modeling of RNA molecules by assembly of recurrent 3D motifs, with the use of low-resolution restraints.…”

Section: Introductionmentioning

confidence: 99%

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

Chojnowski,

Zaborowski,

Magnus

et al. 2023

Bioinformatics

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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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Section: Introductionmentioning

confidence: 99%