iiinova — where your digital self keeps evolving

Eugene F. Baulin @febos.bsky.social · 03/07/2026

We’ve just released a new SQUARNA preprint: doi.org/10.64898/202... Alongside it, we are launching the LaRNAl Platform: larnal.imol.institute #RNA #SQUARNA #LaRNAl #LaRNAlP #Structure #Prediction #Bioinformatics #StructuralBiology #ComputationalBiology

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Eugene F. Baulin @febos.bsky.social · 18/02/2026

Meet SQUARNA 3.0, our tool for #RNA secondary structure prediction: pypi.org/project/SQUA... Now with options for @rfamdb.bsky.social Rfam template search and G-quadruplex pattern recognition! Currently, as CLI and Python API, and soon, a web version. #Rfam #G4 #Gquadruplex #Bioinformatics

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Eugene F. Baulin @febos.bsky.social · 26/09/2025

Meet ClaPNAC - a Classifier of Protein–Nucleic Acid Contacts. ClaPNAC identifies various types of nucleotide-aminoacid contacts in 3D structures of NA-protein complexes. More in the preprint: doi.org/10.1101/2025... #Bioinformatics #Protein #RNA #DNA #Structure #Contact #3D

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Eugene F. Baulin @febos.bsky.social · 29/07/2025

Happy to share, ARTEM is now published in Genome Biology! doi.org/10.1186/s130... 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

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Eugene F. Baulin @febos.bsky.social · 07/07/2025

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: biorxiv.org/content/10.1... #RNA #Structure #3D #GNRA #Tetraloop #Motif #Research #RNAprotein #Interactions

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Eugene F. Baulin @febos.bsky.social · 20/06/2025

#HiringAlert Looking to tackle computational challenges of RNA folding and binding? Come build new RNA algorithms as a #postdoc in my lab! More info: euraxess.ec.europa.eu/jobs/350755 #Academia #Position #Job #Research #RNA #Structure #3D #Bioinformatics #Poland #Warsaw #IMolPAS #NCN

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Eugene F. Baulin @febos.bsky.social · 10/06/2025

📢Job Alert: Postdoctoral Researcher in the Laboratory of RNA Algorithms at imol.institute, up to three years, fully funded by @ncn.gov.pl Details here: euraxess.ec.europa.eu/jobs/350755 #postdoc #Academia #Position #Job #Research #RNA #Structure #Bioinformatics #Poland #Warsaw #IMolPAS #NCN

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Eugene F. Baulin @febos.bsky.social · 27/04/2025

Couldn’t wait to share - SQUARNA 2.0 is here, with greatly improved performance in single-sequence RNA secondary structure prediction! github.com/febos/SQUARNA Updated preprint is coming soon :) #SQUARNA #RNA #2D #Structure #Prediction #Bioinformatics #Research #Pseudoknot

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Eugene F. Baulin @febos.bsky.social · 27/03/2025

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: doi.org/10.1101/2024... #RNA #ARTEM #Kinkturn #Kturn #Motif #Bioinformatics #Science #Research #StructuralBiology

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Eugene F. Baulin @febos.bsky.social · 05/03/2025

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: github.com/david-bogdan... #RNA #DNA #structure #3d #alignment #bioinformatics #research #PDB #tutorial

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Eugene F. Baulin @febos.bsky.social · 07/02/2025

Happy to share, DesiRNA is now published at Nucleic Acids Research! doi.org/10.1093/nar/... 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! #RNA #Design #Research #Bioinformatics #Science #Structure

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Eugene F. Baulin @febos.bsky.social · 07/01/2025

Our ARTEM tool for #RNA #3D #motif search does not rely on annotated pairwise interactions. It could identify a D-loop/T-loop-like motif with 2 non-interacting pyrimidines (U206/U233, right) instead of the characteristic long-range base pair (left). Find out more: doi.org/10.1093/nar/... #research

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Eugene F. Baulin @febos.bsky.social · 11/12/2024

These recurrent RNA "staple" interactions were reported in our recent paper in NAR. They are inherently non-planar and not decomposable into base pairs, therefore remain invisible to existing annotation tools. Find out more: doi.org/10.1093/nar/... #RNA #research #Bioinformatics #motif #Staple

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Eugene F. Baulin @febos.bsky.social · 15/11/2024

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: doi.org/10.1016/j.jm... #RNA #research #Structure #cryoEM #strand #motif #raiA

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Eugene F. Baulin @febos.bsky.social · 10/11/2024

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/SQUARN... BioRxiv: doi.org/10.1101/2023... #RNA #Structure #Bioinformatics #Research #Prediction #2D #pip #Python

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Eugene F. Baulin @febos.bsky.social · 29/10/2024

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: doi.org/10.1101/2024... #rna #dna #3d

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Eugene F. Baulin @febos.bsky.social · 29/09/2024

Happy to share, #ARTEMIS is now published at #NAR! ARTEMIS is a tool for #RNA/#DNA #3D #structure #superposition and structure-based #sequence #alignment. It allowed us to identify an intriguing structural similarity between Lysine and M-box riboswitches! doi.org/10.1093/nar/... #Bioinformatics

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Eugene F. Baulin @febos.bsky.social · 11/09/2024

🧬Our new tool #ARTEM identifies #RNA #3D #motifs based on their isostericity! 🚀Check out kink-turn-like motifs with no kink, and crazy kink-turn variants in group II introns.🔬 doi.org/10.1101/2024... github.com/febos/ARTEM-KT github.com/david-bogdan... #Science #Bioinformatics #Research #Structure

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