AIMC Topic: RNA

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Characterizing ssRNA and dsRNA electrophoretic behavior: empirical insights with neural network-aided predictions.

The Analyst Aug 4, 2025
RNA-based therapeutics are currently at the forefront of the biopharmaceutical industry because of their safety, efficacy, and shortened time from disease discovery to therapy development. Microfluidic electrophoresis provides a great analytical plat...
RNA, Double-Stranded Humans Electrophoresis Neural Networks, Computer Microfluidic Analytical Techniques RNA
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m5U-HybridNet: Integrating an RNA Foundation Model with CNN Features for Accurate Prediction of 5-Methyluridine Modification Sites.

Journal of chemical information and modeling Jul 22, 2025
The 5-methyluridine (m5U) modification in RNA is vital for numerous biological processes, making its precise identification a key focus in computational biology. However, traditional wet-lab detection methods are cumbersome and time-consuming, wherea...
Neural Networks, Computer RNA Uridine Deep Learning Computational Biology
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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 Nucleotide Motifs RNA Nucleic Acid Conformation Cluster Analysis
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Interpretability-guided RNA N-methyladenosine modification site prediction with invertible neural networks.

Communications biology Jul 8, 2025
As one of the most common and abundant post-transcriptional modifications, N-methyladenosine (mA) has been extensively studied for its essential regulatory role in gene expression and cell functions. The location of mA RNA modification sites, however...
RNA Methylation Adenosine RNA Processing, Post-Transcriptional Deep Learning Computational Biology Animals Humans Neural Networks, Computer
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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 Natural Language Processing Computational Biology Nucleic Acid Conformation Models, Molecular
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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...
Nucleic Acid Conformation Machine Learning Computational Biology Algorithms RNA
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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, Untranslated Deep Learning RNA Computational Biology Nucleic Acid Conformation Sequence Analysis, RNA
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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...
RNA Nucleic Acid Conformation Base Pairing Nucleotide Motifs Deep Learning Computational Biology Thermodynamics
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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...
Molecular Docking Simulation RNA Neural Networks, Computer Machine Learning Nucleic Acid Conformation Small Molecule Libraries
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Explainable RNA-Small Molecule Binding Affinity Prediction Based on Multiview Enhancement Learning.

Journal of chemical information and modeling Jun 3, 2025
RNA has the potential to serve as a drug target, requiring RNA-small molecule binding affinity to screen potential drugs generally. However, accurately predicting RNA-small molecule binding affinity remains a highly challenging task. This study propo...
RNA Deep Learning Small Molecule Libraries
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