AIMC Topic: Nucleic Acid Conformation

Clear Filters Showing 1 to 10 of 116 articles

How large is the universe of RNA-like motifs? A clustering analysis of RNA graph motifs using topological descriptors.

PLoS computational biology Jul 15, 2025
Identifying novel and functional RNA structures remains a significant challenge in RNA motif design and is crucial for developing RNA-based therapeutics. Here we introduce a computational topology-based approach with unsupervised machine-learning alg...
Algorithms Computational Biology Nucleic Acid Conformation Nucleotide Motifs Cluster Analysis RNA
View on PubMed DOI

Predicting RNA Structure Utilizing Attention from Pretrained Language Models.

Journal of chemical information and modeling Jul 2, 2025
RNA possesses functional significance that extends beyond the transport of genetic information. The functional roles of noncoding RNA can be mediated through their tertiary and secondary structure, and thus, predicting RNA structure holds great promi...
RNA Nucleic Acid Conformation Natural Language Processing Models, Molecular Computational Biology
View on PubMed DOI

Predict the degree of secondary structures of the encoding sequences in DNA storage by deep learning model.

Scientific reports Jul 1, 2025
DNA storage has been widely considered as a promising alternative for exponentially growing data. However, the inherent complex secondary structures severely compromise the processes of synthesis, PCR amplification, and sequencing, interfering with r...
Nucleic Acid Conformation Deep Learning DNA
View on PubMed DOI

Comprehensive datasets for RNA design, machine learning, and beyond.

Scientific reports Jul 1, 2025
RNA molecules are essential in regulating biological processes such as gene expression, cellular differentiation, and development. Accurately predicting RNA secondary structures and designing sequences that fold into specific configurations remain si...
Machine Learning Algorithms Nucleic Acid Conformation Computational Biology RNA
View on PubMed DOI

RiNALMo: general-purpose RNA language models can generalize well on structure prediction tasks.

Nature communications Jul 1, 2025
While RNA has recently been recognized as an interesting small-molecule drug target, many challenges remain to be addressed before we take full advantage of it. This emphasizes the necessity to improve our understanding of its structures and function...
Software RNA Computational Biology Nucleic Acid Conformation Deep Learning RNA, Untranslated Sequence Analysis, RNA
View on PubMed DOI

Quantifying complexity in DNA structures with high resolution Atomic Force Microscopy.

Nature communications Jul 1, 2025
DNA topology is essential for regulating cellular processes and maintaining genome stability, yet it is challenging to quantify due to the size and complexity of topologically constrained DNA molecules. By combining high-resolution Atomic Force Micro...
Animals Nucleic Acid Conformation Xenopus laevis Microscopy, Atomic Force Plasmids DNA Replication Escherichia coli DNA
View on PubMed DOI

Deep generalizable prediction of RNA secondary structure via base pair motif energy.

Nature communications Jul 1, 2025
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...
Base Pairing Nucleotide Motifs Thermodynamics RNA Nucleic Acid Conformation Computational Biology Deep Learning
View on PubMed DOI

AffiGrapher: Contrastive Heterogeneous Graph Learning with Aromatic Virtual Nodes for RNA-Small Molecule Binding Affinity Prediction.

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...
Neural Networks, Computer Nucleic Acid Conformation Machine Learning Small Molecule Libraries Molecular Docking Simulation RNA
View on PubMed DOI

Melting Profile of DNA in Crowded Solution: Model-Based Study.

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 ...
Molecular Dynamics Simulation Nucleic Acid Conformation DNA Solutions Nucleic Acid Denaturation
View on PubMed DOI

Loop Nucleotide Chemical Shifts as a Tool to Characterize DNA G-Quadruplexes.

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...
Nucleotides Nucleic Acid Conformation Machine Learning DNA G-Quadruplexes Nuclear Magnetic Resonance, Biomolecular Magnetic Resonance Spectroscopy
View on PubMed DOI
Popular Topics
Recent Journals