The RNA 3D Motif Atlas: Computational methods for extraction, organization and evaluation of RNA motifs

LG Parlea, BA Sweeney, M Hosseini-Asanjan… - Methods, 2016 - Elsevier
RNA 3D motifs occupy places in structured RNA molecules that correspond to the hairpin,
internal and multi-helix junction “loops” of their secondary structure representations. As …

Analyzing and building nucleic acid structures with 3DNA

AV Colasanti, XJ Lu, WK Olson - Journal of visualized …, 2013 - pmc.ncbi.nlm.nih.gov
The 3DNA software package is a popular and versatile bioinformatics tool with capabilities
to analyze, construct, and visualize three-dimensional nucleic acid structures. This article …

In silico optimization of RNA–protein interactions for CRISPR-Cas13-based antimicrobials

H Park, Y Park, U Berani, E Bang, J Vankerschaver… - Biology Direct, 2022 - Springer
RNA–protein interactions are crucial for diverse biological processes. In prokaryotes, RNA–
protein interactions enable adaptive immunity through CRISPR-Cas systems. These …

A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures

DR Bohdan, VV Voronina, JM Bujnicki… - Nucleic acids …, 2023 - academic.oup.com
Understanding the 3D structure of RNA is key to understanding RNA function. RNA 3D
structure is modular and can be seen as a composition of building blocks of various sizes …

Topology independent comparison of RNA 3D structures using the CLICK algorithm

MN Nguyen, AYL Sim, Y Wan… - Nucleic acids …, 2017 - academic.oup.com
RNA molecules are attractive therapeutic targets because non-coding RNA molecules have
increasingly been found to play key regulatory roles in the cell. Comparing and classifying …