Lmst

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: https://doi.org/10.1101/2025.05.30.657037

#Bioinformatics #Protein #RNA #DNA #Structure #Contact #3D

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

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://biorxiv.org/content/10.1101/2025.07.03.663028v1

#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: https://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 https://imol.institute/, up to three years, fully funded by https://ncn.gov.pl/en

Details here: https://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!

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

#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:

https://github.com/david-bogdan-r/ARTEMIS/blob/main/ARTEMIS_TUTORIAL_v1.51.pdf

#RNA #DNA #structure #3d #alignment #superposition #bioinformatics #structuralbiology #science #research #PDB #tutorial

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!

#RNA #Design #Research #Bioinformatics #Science #Structure

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

#RNA #research #science #Bioinformatics #ARTEM #motif #structure #3d #DloopTloop #Basepair #longrange

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

#RNA #research #science #Bioinformatics #structure #motif #Staple #Basepair #Interaction

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

#RNA #research #science #Structure #structuralbiology #cryoEM #junction #tetraloop #strand #motif #Dloop #Tloop #GAAA #GNRA #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:
https://github.com/febos/SQUARNA/blob/main/demo.ipynb

BioRxiv:
https://doi.org/10.1101/2023.08.28.555103

#RNA #Structure #Science #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:
https://doi.org/10.1101/2024.05.31.596898

#rna #dna #3d #science #structure #structuralbiology #bioinformatics #research #isostericity #motif #artem #junction #helix #module

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. It allowed us to identify an intriguing structural similarity between Lysine and M-box riboswitches (see the figure).

ARTEMIS is available at GitHub:

https://github.com/david-bogdan-r/ARTEMIS

#RNA #DNA #3D #Science #Bioinformatics #StructuralBiology #Research #Innovation #Structure #Topology #Sequence #Superposition #Alignment