| Home page | https://imol.institute/leaders/baulin-group/ |
| Google Scholar | https://scholar.google.com/citations?user=sjfDaUwAAAAJ&hl=en |
| https://x.com/febos41 | |
| ORCID | https://orcid.org/0000-0003-4694-9783 |
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
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!
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
The functions of non-coding RNAs are largely defined by their three-dimensional structures. RNA 3D structure is organized hierarchically and consists of recurrent building blocks called tertiary motifs. The computational problem of RNA tertiary motif search remains largely unsolved, as standard approaches are restrained by sequence, interaction network, or backbone topology. We developed the ARTEM superposition algorithm, which is free from these limitations. Here, we present a version of ARTEM that allows automated searches of RNA and DNA structure databases to identify 3D structure motifs. We exemplify it by a search of motifs isosteric to the kink-turn motif. This widespread motif plays a role in many aspects of RNA function, and its mutations are known to cause several human syndromes. With ARTEM, we 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. Additionally, we 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 and DNA 3D folds and motifs and analyze their correlations and variations. ### Competing Interest Statement The authors have declared no competing interest.
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!
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
