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

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

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

#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

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

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

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

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

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