Eugene F. Baulin

I develop innovative algorithms and best-in-class tools for RNA computational structural biology: https://imol.institute/leaders/baulin-group/

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Happy to share a new SQUARNA preprint and a companion web resource from our group at IMol.We’ve just released a new SQUARNA preprint:https://doi.org/10.64898/2026.06.30.735492 Alongside it, we are launching the LaRNAl Platform:https://larnal.imol.institute/ SQUARNA is an RNA 2D structure prediction method based on a variant of the base pair maximization framework. It supports both single-sequence and alignment-based prediction and can handle pseudoknotted structures as well as alternative conformations. It also integrates structural restraints and chemical probing data and can identify Rfam templates, G-quadruplex patterns, and even protein-binding motifs!The method is implemented through multiple algorithmic variants, including the classical Nussinov algorithm, which shows state-of-the-art performance with our scoring scheme, and the Edmonds algorithm, a polynomial-time approach for pseudoknot prediction (yes - it’s not NP-hard under base pair maximization!).The LaRNAl Platform currently provides a web interface for SQUARNA, enabling analysis of individual RNA sequences with beautiful 2D visualizations powered by RFviewJS (https://github.com/dincarnato/RFviewJS) by Danny Incarnato and RNAcanvas (https://github.com/pzhaojohnson/rnacanvas).More tools from the lab will be integrated into the platform soon, including R3FOLD, our upcoming RNA 3D structure prediction method, expected in late 2026.Feedback and discussion are very welcome, and stay tuned for more!Many thanks to Maksim Serdakov (IMol), Grigory Nikolaev, Davyd Bohdan, and Janusz Bujnicki (International Institute of Molecular and Cell Biology in Warsaw), and of course EMBO and NCN National Science Centre!#RNA #SQUARNA #LaRNAl #LaRNAlP #Structure #Prediction #Bioinformatics #StructuralBiology #ComputationalBiology

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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!

#Research #Bioinformatics #3D #RNA #DNA #Motifs #ARTEM

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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

#RNA #Structure #3D #GNRA #Tetraloop #Motif #Research #RNAprotein #Interactions

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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

Meet ClaPNAC - a Classifier of Protein–Nucleic Acid Contacts.

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#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

#Academia #Position #Job #Research #RNA #Structure #3D #Bioinformatics #Poland #Warsaw #IMolPAS #NCN

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📢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

#Postdoc #Academia #Position #Job #Research #RNA #Structure #Bioinformatics #Poland #Warsaw #IMolPAS #NCN

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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

SQUARNA 2.0

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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

#RNA #ARTEM #Kinkturn #Kturn #Motif #Bioinformatics #Science #Research #StructuralBiology

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Our ARTEMIS tool for aligning 3D structures of nucleic acids is now equipped with a detailed Tutorial, covering structure searches, sub-optimal matches, and even PDB/CIF conversion, check it out: https://github.com/david-bogdan-r/ARTEMIS/blob/main/ARTEMIS_TUTORIAL_v1.51.pdf

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Happy to share, DesiRNA is now published at Nucleic Acids Research! https://doi.org/10.1093/nar/gkae1306 DesiRNA is a tool for RNA sequence design (inverse folding) and it is the first to solve all 100 puzzles in the Eterna100 benchmark within 24 h!

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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).

Find out more: https://doi.org/10.1093/nar/gkad605

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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