Deep learning methods have demonstrated great performance for RNA secondary structure prediction. However, generalizability is a common unsolved issue on unseen out-of-distribution RNA families, which hinders further improvement of the accuracy and r...
Aptamers are oligonucleotide receptors that bind to their targets with high affinity. Here, we consider aptamers comprised of single-stranded DNA that undergo target-binding-induced conformational changes, giving rise to unique secondary and tertiary...
Journal of chemical information and modeling
Jun 26, 2025
RNA molecules exhibit diverse structures and functions, making them promising drug targets. However, predicting RNA-small molecule binding affinity remains challenging due to limited experimental data and the structural variability introduced by mult...
International journal of molecular sciences
May 31, 2025
Recent advances in molecular dynamics (MD) simulations and the introduction of artificial intelligence (AI) have resulted in a significant increase in accuracy for structure prediction. However, the cell is a highly crowded environment consisting of ...
Chemphyschem : a European journal of chemical physics and physical chemistry
May 7, 2025
DNA G-quadruplexes are known to play myriad functional roles in the cellular context and their structural diversity has diverse applications in various fields of science. Solution-state NMR spectroscopy has been instrumental in characterization of DN...
RNA is a remarkably versatile molecule that has been engineered for applications in therapeutics, diagnostics, and in vivo information-processing systems. However, the complex relationship between the sequence, structure, and function of RNA often ne...
Ribonucleic acid (RNA) structural motif identification is a crucial step for understanding RNA structure and functionality. Due to the complexity and variations of RNA 3D structures, identifying RNA structural motifs is challenging and time-consuming...
The accurate prediction of RNA secondary structure, and pseudoknots in particular, is of great importance in understanding the functions of RNAs since they give insights into their folding in three-dimensional space. However, existing approaches ofte...
Riboswitches are a class of noncoding RNA structures that interact with target ligands to cause a conformational change that can then execute some regulatory purpose within the cell. Riboswitches are ubiquitous and well characterized in bacteria and ...
International journal of biological macromolecules
Apr 21, 2025
Biological interactions between RNA and small-molecule ligands play a crucial role in determining the specific functions of RNA, such as catalysis and folding, and are essential for guiding drug design in the medical field. Accurately predicting the ...
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