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. 2022 Jul 5;50(W1):W663-W669.
doi: 10.1093/nar/gkac218.

RNAspider: a webserver to analyze entanglements in RNA 3D structures

Kamil Luwanski  1 , Vladyslav Hlushchenko  1 , Mariusz Popenda  2 , Tomasz Zok  1 , Joanna Sarzynska  2 , Daniil Martsich  1 , Marta Szachniuk  1   2 , Maciej Antczak  1   2
Affiliations

RNAspider: a webserver to analyze entanglements in RNA 3D structures

Kamil Luwanski et al. Nucleic Acids Res. .

Abstract

Advances in experimental and computational techniques enable the exploration of large and complex RNA 3D structures. These, in turn, reveal previously unstudied properties and motifs not characteristic for small molecules with simple architectures. Examples include entanglements of structural elements in RNA molecules and knot-like folds discovered, among others, in the genomes of RNA viruses. Recently, we presented the first classification of entanglements, determined by their topology and the type of entangled structural elements. Here, we introduce RNAspider - a web server to automatically identify, classify, and visualize primary and higher-order entanglements in RNA tertiary structures. The program applies to evaluate RNA 3D models obtained experimentally or by computational prediction. It supports the analysis of uncommon topologies in the pseudoknotted RNA structures. RNAspider is implemented as a publicly available tool with a user-friendly interface and can be freely accessed at https://rnaspider.cs.put.poznan.pl/.

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Figures

Graphical Abstract
Graphical Abstract
RNAspider: a webserver to analyze entanglements in RNA 3D structures.
Figure 1.
Figure 1.
Classification of entanglements of structure elements shown on the example of entangled RNA hairpins: (A) interlaces and (B) lassos.
Figure 2.
Figure 2.
Single strand S punctures a closed element L (A) once, (B) twice or (C) three times, forming L(S), L(S.) or L(S..)-type entanglement.
Figure 3.
Figure 3.
Entanglement of type D(S) –dinucleotide step lassoing the single-stranded fragment – from RNAComposer-5UTR model shown as (A) a full-atom representation, (B) a simplified view from RNAspider and (C) a 2D structure with highlighted elements forming the entanglement.
Figure 4.
Figure 4.
Higher-order L(S) entanglement in a knot-like fold (PDB ID: 7K16) visualized by RNAspider in (A) full-atom and (B) simplified representation. The red bead indicates the point of puncturing the surface spanned on the loop by the polygonal chain of the 5′-end. The point of intersection falls between the C4′ atom of residue 2 and the P atom of residue 3 of the polygonal chain.
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