Eugene F. Baulin

Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16 Biomolecules rely on water and ions for stable folding, but these interactions are often transient, dynamic, or disordered and thus hidden from experiments and evaluation challenges that represent bio...

A recent manuscript describing our and others’ efforts to predict the solvation shell of a group I intron is now available on bioRxiv! 🔬 doi.org/10.1101/2025...

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

ARTEM: a method for RNA and DNA tertiary motif identification with backbone permutations - Genome Biology Non-coding RNA functions are largely defined by their 3D structures, which consist of recurrent building blocks, tertiary motifs. The computational motif search problem remains largely unsolved, as standard approaches are restrained by sequence, interactions, or backbone topology. We present ARTEM 2.0, which enables automated, unrestrained searches of RNA and DNA structure databases to identify 3D motifs. We apply ARTEM for searching kink-turns, G-quadruplexes, GNRA tetraloops, and i-motifs. ARTEM outperforms existing methods and enables the discovery of novel motif variants. ARTEM opens a fundamentally new way of studying nucleic acid 3D folds and motifs and analyzing their correlations and variations.

An article published in Genome Biology presents ARTEM 2.0: a method which enables automated, unrestrained searches of RNA and DNA structure databases to identify 3D motifs.

#MedSky #STS

Thanks to @iimcb.bsky.social, imol.institute, @ncn.gov.pl, @embo.org, @jmbujnicki.bsky.social, and all the co-authors!

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

Thanks to @jmbujnicki.bsky.social @iimcb.bsky.social, and imol.institute

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

📢#Job Alert:
The Lab of #RNA #Algorithms @ imol.institute
has an open position for a #PostDoc interested in RNA computational biology.

Apply before July 10th: euraxess.ec.europa.eu/jobs/350755

Please spread the word!

#Academia #Position #Research #Bioinformatics #Poland #Warsaw #Hiring

#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

📢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

ClaPNAC: a Classifier of Protein - Nucleic Acid Contacts https://www.biorxiv.org/content/10.1101/2025.05.30.657037v1

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

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

Group leaders (multiple positions) Extended deadline: March 24, 2025. More Information

The International Institute of Molecular Mechanisms and Machines Polish Academy of Sciences (IMol) seeks candidates for Group Leader positions.
Extended deadline: March 24, 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

I’m happy to have contributed a tiny part to this exciting research!

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

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

Wow, thanks! I'll keep this in mind for my next tools!

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

RNA-Puzzles Round V: blind predictions of 23 RNA structures - Nature Methods The results of the Fifth RNA-Puzzles contest highlights advances in RNA three-dimensional structure prediction and uncovers new insights into RNA folding and structure.

RNA-Puzzles Round V paper is out:
www.nature.com/articles/s41...
It reports the evaluation of blind prediction of 23 targets predicted by 18 groups worldwide. I'm glad that our group ranked as one of the top four groups in this competition!

#RNA #prediction #RNApuzzles #CASP16

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

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

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

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

🧬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