I develop innovative algorithms and best-in-class tools for RNA computational structural biology: https://github.com/febos/wikiMy research interests lie in the broad field of computational methods, including artificial intelligence methods, applied to the studies of RNA structure organization and mechanisms of RNA folding and functioning.
Don't wanna be here? Send us removal request.
Text
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
0 notes
Text
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/SQUARNA/blob/main/demo.ipynb
BioRxiv: doi.org/10.1101/2023.08.28.555103
0 notes
Text
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?馃 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
0 notes
Text
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. Our benchmarks show that it outperforms the existing tools for both sequentially-ordered and topology-independent alignment.
ARTEMIS allowed us to identify an intriguing structural similarity between Lysine and M-box riboswitches (see the figure) and to describe the minor-groove/minor-groove helical packing motif. ARTEMIS is the first tool able to report several alternative superpositions, which makes it suitable for structural motif identification tasks.
ARTEMIS is available at GitHub: https://github.com/david-bogdan-r/ARTEMIS
Thanks to Davyd Bohdan, Janusz Bujnicki, & International Institute of Molecular and Cell Biology in Warsaw!
#rna#dna#3d#science#bioinformatics#structuralbiology#research#innovation#structure#topology#sequence#superposition#alignment
5 notes
路
View notes
Text
ARTEM: THE tool for RNA 3D motif identification, with backbone permutations!
ARTEM identifies RNA tertiary motifs based purely on their isostericity. We applied it to search for kink-turn-like motifs and 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 (see the Figure). We also 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 3D folds and motifs and analyze their correlations and variations.
Want to learn more? - Check out our preprint on bioRxiv doi.org/10.1101/2024.05.31.596898 - ARTEM is available for you on GitHub https://github.com/david-bogdan-r/ARTEM https://github.com/febos/ARTEM-KT
#rna#science#bioinformatics#structuralbiology#research#innovation#algorithms#biology#motif#3D#structure#kinkturn#kjunction#ARTEM#permutation#permutations
0 notes
Text
Our works on RNA structure analysis and prediction.
2 notes
路
View notes