Eugene F. Baulin

Happy to share, ARTEM is now published in Genome Biology! https://doi.org/10.1186/s13059-025-03696-2 ARTEM enables screening RNA and DNA 3D structure databases for arbitrary 3D motifs. Kink-turns, G-quadruplexes, GNRA tetraloops, i-motifs, you name it!

Turns out RNA can make a GNRA tetraloop-like motif out of almost anything! Like in these pentaloops, whose looped-out bases interact with proteins.

Read the preprint: https://doi.org/10.1101/2025.07.03.663028

ClaPNAC identifies various types of nucleotide-aminoacid contacts in 3D structures of NA-protein complexes. More in the preprint: https://doi.org/10.1101/2025.05.30.657037

#HiringAlert

Looking to tackle computational challenges of RNA folding and binding?

Come build new RNA algorithms as a #postdoc in my lab!

More info: https://euraxess.ec.europa.eu/jobs/350755

📢Job Alert: Postdoctoral Researcher in the Laboratory of RNA Algorithms @IMol_Institute, up to three years, fully funded by @NCN_PL

Details here: https://euraxess.ec.europa.eu/jobs/350755

Couldn’t wait to share - SQUARNA 2.0 is here, with greatly improved performance in single-sequence RNA secondary structure prediction!

https://github.com/febos/SQUARNA

Updated preprint is coming soon :)

#SQUARNA #RNA #2D #Structure #Prediction #Bioinformatics #Research #Pseudoknot

The coordination loop in group II introns forms a chimeric kink-turn that involves a long-range base pair (A251-U326).

More weird kink-turns in our recent preprint: https://doi.org/10.1101/2024.05.31.596898

Our ARTEM tool for RNA 3D motif search does not rely on annotated pairwise interactions. Thus, it could identify a D-loop/T-loop-like motif with two non-interacting pyrimidines (U206/U233, right) instead of the characteristic long-range base pair (left).

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:

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?

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

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!

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.