febos

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These recurrent RNA "staple" interactions were reported in our recent paper in Nucleic Acids Research. They are inherently non-planar and not decomposable into base pairs and, therefore remain invisible to existing annotation tools.

Find out more:

https://doi.org/10.1093/nar/gkad605

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In the raiA ncRNA structure that we recently determined, we identified a junction strand (B) that mimics both the GAAA-tetraloop (A) AND the D-loop/T-loop interaction motif (C) - how cool is that?

Find out more: https://doi.org/10.1016/j.jmb.2024.168833

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Now it's that simple to predict RNA secondary structure with SQUARNA Python3 library:

pip install SQUARNA

import SQUARNA SQUARNA.Predict(inputseq="CCCGNRAGGG")

Demo: github.com/febos/SQUARNA/blob/main/demo.ipynb

BioRxiv: doi.org/10.1101/2023.08.28.555103

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These are two RNA 3D structure modules: one is a long-range helix-helix interface and another is a four-way junction loop, but can you spot the difference?🧐 Find out which is which in our recent preprint on RNA tertiary motif search and their isostericity: https://doi.org/10.1101/2024.05.31.596898

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Happy to share, ARTEMIS is now published at NAR!

https://doi.org/10.1093/nar/gkae758

ARTEMIS is a new tool for RNA/DNA 3D structure superposition and structure-based sequence alignment. Our benchmarks show that it outperforms the existing tools for both sequentially-ordered and topology-independent alignment.

ARTEMIS allowed us to identify an intriguing structural similarity between Lysine and M-box riboswitches (see the figure) and to describe the minor-groove/minor-groove helical packing motif. ARTEMIS is the first tool able to report several alternative superpositions, which makes it suitable for structural motif identification tasks.

ARTEMIS is available at GitHub: https://github.com/david-bogdan-r/ARTEMIS

Thanks to Davyd Bohdan, Janusz Bujnicki, & International Institute of Molecular and Cell Biology in Warsaw!

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ARTEM: THE tool for RNA 3D motif identification, with backbone permutations!

ARTEM identifies RNA tertiary motifs based purely on their isostericity. We applied it to search for kink-turn-like motifs and discovered two new kink-turn topologies, multiple no-kink variants of the motif, and showed that a ribosomal junction in bacteria forms either a kink or a no-kink variant depending on the species (see the Figure). We also identified kink-turns in the catalytic core of group II introns, whose structures have not previously been characterized as containing kink-turns.

ARTEM opens a fundamentally new way to study RNA 3D folds and motifs and analyze their correlations and variations.

Want to learn more? - Check out our preprint on bioRxiv doi.org/10.1101/2024.05.31.596898 - ARTEM is available for you on GitHub https://github.com/david-bogdan-r/ARTEM https://github.com/febos/ARTEM-KT

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Our works on RNA structure analysis and prediction.