NCN @ncn.gov.pl project spotlight 🔬
We investigate how mRNA folds in vivo, how its structure changes across the cell, and how RNA structure regulates gene expression in yeast. #RNA #mRNA #RNAstructure #GeneExpression #Yeast

Hi Bluesky — welcome to KPW Lab!
We are interested in how #RNAstructure influences function, stability, and interactions in the cell.
Our work connects experimental #RNA structure probing with structural modeling and #bioinformatics. We’re excited to share our science, publications, and tools here.

Top: A representative modeling example from Chimpanzee CPEB3 HDV-like ribozyme (PDB ID: 7QR3), with models predicted by four better-performing methods (blue cartoons) overlaid on experimental structure (gray cartoons). Left to right: DRFold2, DeepFoldRNA, AlphaFold3, RhoFold. Bottom: Structural visualization of the example from coxsackievirus B3 cloverleaf RNA (PDBID: 8DP3), showing experimental structure (left), AlphaFold3’s best prediction from 100 models (middle), and 5th model of DRfold2 (right), respectively. Structures are rainbow-colored from 5′ (blue) to 3′ (red) end.

Accurate RNA structure prediction remains a challenge, despite recent computational advances. This study presents DRFold2, a #DeepLearning framework that significantly enhances accuracy of de novo #RNAstructure prediction by increasing contact prediction precision @plosbiology.org 🧪 plos.io/4aoOQiX

Top: A representative modeling example from Chimpanzee CPEB3 HDV-like ribozyme (PDB ID: 7QR3), with models predicted by four better-performing methods (blue cartoons) overlaid on experimental structure (gray cartoons). Left to right: DRFold2, DeepFoldRNA, AlphaFold3, RhoFold. Bottom: Structural visualization of the example from coxsackievirus B3 cloverleaf RNA (PDBID: 8DP3), showing experimental structure (left), AlphaFold3’s best prediction from 100 models (middle), and 5th model of DRfold2 (right), respectively. Structures are rainbow-colored from 5′ (blue) to 3′ (red) end.

Accurate RNA structure prediction remains a challenge, despite recent computational advances. This study presents DRFold2, a #DeepLearning framework that significantly enhances accuracy of de novo #RNAstructure prediction by increasing contact prediction precision @plosbiology.org 🧪 plos.io/4aoOQiX

Top: A representative modeling example from Chimpanzee CPEB3 HDV-like ribozyme (PDB ID: 7QR3), with models predicted by four better-performing methods (blue cartoons) overlaid on experimental structure (gray cartoons). Left to right: DRFold2, DeepFoldRNA, AlphaFold3, RhoFold. Bottom: Structural visualization of the example from coxsackievirus B3 cloverleaf RNA (PDBID: 8DP3), showing experimental structure (left), AlphaFold3’s best prediction from 100 models (middle), and 5th model of DRfold2 (right), respectively. Structures are rainbow-colored from 5′ (blue) to 3′ (red) end.

Accurate RNA structure prediction remains a challenge, despite recent computational advances. This study presents DRFold2, a #DeepLearning framework that significantly enhances accuracy of de novo #RNAstructure prediction by increasing contact prediction precision @plosbiology.org 🧪 plos.io/4aoOQiX

Exploring GNRA tetraloop-like motifs in nucleic acid 3D structures - Scientific Reports Scientific Reports - Exploring GNRA tetraloop-like motifs in nucleic acid 3D structures

A comprehensive survey of GNRA tetraloop-like motifs reveals 12 recurrent backbone topology variants, including pentaloop and multi-strand forms, revealing frequent protein interactions. #MotifDesign #RNAstructure #Bioinformatics 🧬📐
📄 doi.org/10.1038/s415...
👤 EVBC: Janusz Bujnicki

Unlocking the regulatory code of RNA: launching the Human RNome Project - Genome Biology The human RNome, the complete set of RNA molecules in human cells, arises through complex processing and includes diverse molecular species. While research traditionally focuses on four canonical nucl...

Exciting news for the RNA research community!

The Human RNome Project has been launched: a global effort to map all human RNAs and their chemical modifications. Proud to support it and contribute to the article in Genome Biology doi.org/10.1186/s130...
#RNA #bioinformatics #RNAstructure #modomics

📣 Don't miss this new Review!

Interplay between RNA-protein interactions and RNA structures in gene regulation

🔓 buff.ly/pu6TpVa

🖊️ @rnaminni.bsky.social

#RBPs #RNA #RNAbiology #RNAbindingproteins #RNAbinding #RNAstructure

Today I tested my own method for RNA analysis. This method can serve as an early indicator of RNA stability, even before detailed 3D modeling.

#Bioinformatics #ComputationalBiology #StructuralBiology #MolecularBiology #RNA #Biotechnology #LifeSciences #RNAresearch #RNAstructure #RNAfolding #LLM

(2/8) Predicting full 3D #RNAstructure remains extremely hard — even with AI.

Recent benchmarks show deep-learning tools still struggle on novel RNAs (c.f. Bahai et al, 2024, PLoS Comp Bio)

And while AlphaFold 3 can model RNA, its accuracy lags far behind proteins: www.ebi.ac.uk/training/onl...

SEISMICgraph: a web-based tool for RNA structure data visualization. #RNAstructure #WebTool #DataVisualization #Bioinformatics @narjournal.bsky.social
academic.oup.com/nar/article/...

Calling #RNA & #Virology researchers! 🧬🦠
Submissions are open for the open-access Special Issue '𝗙𝘂𝗻𝗰𝘁𝗶𝗼𝗻𝗮𝗹 𝗥𝗡𝗔𝘀 𝗶𝗻 𝗩𝗶𝗿𝗼𝗹𝗼𝗴𝘆' in MDPI Viruses, which I'm guest editing.
📝 Original research & reviews welcome!
🗓️ Deadline: Feb 28, 2026
michaelwolfinger.com/blog/2025/bl...
#FunctionalRNA #RNAstructure

Super new work from Chris and the team, including some cool #smFRET showing changes to n #RNAstructure- have a read!

I am in San Diego attending the #RNA25 annual meeting @rnasociety.bsky.social! Whether you work with #RNAstructure, are curious about ways to study it or have a favourite RNA that you would like to explore come to visit poster number 431 tonight! @miskalab.bsky.social

a black and white drawing of a clock that says 11:18 ALT: a black and white drawing of a clock that says 11:18

🧬 RNA is far more than just a blueprint for proteins! Its shape is crucial to its function. But how do we study RNA's complex structure?
🔍 Find out at the 20th March RNA Club as we dive into groundbreaking techniques that are changing the game in RNA research!
#RNAstructure #RNA

DesiRNA: structure-based design of RNA sequences with a replica exchange Monte Carlo approach Abstract. Designing RNA sequences that form a specific structure remains a challenge. Current computational methods often struggle with the complexity of R

🚀 DesiRNA, our new RNA design tool, solved all 100 puzzles in the Eterna100 benchmark within 24 hours, outperforming all existing RNA design programs! 🧬

🔗 Read about it in Nucleic Acids Research: doi.org/10.1093/nar/...

#Science #Bioinformatics #ComputationalBiology #RNA #RNAstructure

New Methods for RNA Modification Detection and Structure Probing In this webinar, you’ll hear from three experts in the field about their research into the structure, function, regulation and detection of RNA modifications.

Missed our recent webinar on New Methods for RNA Modification Detection and Structure Probing?

Explore innovative techniques that are transforming our understanding of #RNAmods and #RNAstructure.

Watch here: bit.ly/3TULhbr

#RNA #RNASky #structuralRNA

Did you know? The #ViennaRNA Package can handle a wide range of RNA modifications, including:

#Inosine (I)
#Pseudouridine (P)
#N6-methyladenosine (m6A)
#7-deaza-adenosine (7DA)
#Nebularine (purine)
#Dihydrouridine (D)

#Bioinformatics #ComputationalBiology #RNAStructure #SyntheticBiology
4/n

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 tackles RNA 3D structure prediction with 23 challenging targets from viral and non-viral origins, setting new benchmarks for RNA bioinformatics. 🧬📊
#Bioinformatics #RNAstructure #ComputationalBiology

📄 doi.org/10.1038/s415...
EVBC👤: Tomasz K Wirecki

Rapid folding of nascent RNA regulates eukaryotic RNA biogenesis An RNA′s catalytic, regulatory, or coding potential depends on RNA structure formation. Because base pairing occurs during transcription, early structural states can govern RNA processing events and d...

Super method linking GROseq/DMSMaPseq shedding light on co-transcriptional #RNA folding. Really enjoyed seeing this presented recently. #RNAStructure www.biorxiv.org/content/10.1...

This looks useful- will give it a go #RNAstructure

Could I be added to RNA Biology?
as #RNAstructure and #RNAfunction relationship fan 🫶🙃

Hi! 👋 I'm new here 👋
I recently defended my PhD and I'm loved in #RNA structures in vivo 🫶 Very excited to share my two articles at NAR (results of my PhD)!
1📎 academic.oup.com/nar/article/...
2📎 academic.oup.com/nar/article/...
The first #RNAstructure of Ty1 and Ty3 LTR #retrotransposon genomes!

.@AGbioDS from http://RNAfold.ai closing off this session of the @UNSWRNA annual symposium presenting his (and @oncogenie's) company, that leverages #AI to design new therapies targeting #RNAstructure and accessibility.