AIMC Topic: RNA

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Definer: A computational method for accurate identification of RNA pseudouridine sites based on deep learning.

PloS one Apr 24, 2025
Pseudouridine is an important modification site, which is widely present in a variety of non-coding RNAs and is involved in a variety of important biological processes. Studies have shown that pseudouridine is important in many biological functions s...
Computational Biology RNA Saccharomyces cerevisiae Pseudouridine Deep Learning Humans Mice Animals
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The prediction of RNA-small molecule binding sites in RNA structures based on geometric deep learning.

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 ...
Small Molecule Libraries Nucleic Acid Conformation Binding Sites Deep Learning RNA Computational Biology Models, Molecular Ligands
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RPI-GGCN: Prediction of RNA-Protein Interaction Based on Interpretability Gated Graph Convolution Neural Network and Co-Regularized Variational Autoencoders.

IEEE transactions on neural networks and learning systems Apr 4, 2025
RNA-protein interactions (RPIs) play an important role in several fundamental cellular physiological processes, including cell motility, chromosome replication, transcription and translation, and signaling. Predicting RPI can guide the exploration of...
Neural Networks, Computer Algorithms Computational Biology Humans RNA Autoencoder RNA-Binding Proteins Proteins
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Critical Assessment of RNA and DNA Structure Predictions via Artificial Intelligence: The Imitation Game.

Journal of chemical information and modeling Mar 30, 2025
Computational predictions of biomolecular structure via artificial intelligence (AI) based approaches, as exemplified by AlphaFold software, have the potential to model of all life's biomolecules. We performed oligonucleotide structure prediction and...
Artificial Intelligence DNA RNA Models, Molecular Nucleic Acid Conformation
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RNAmigos2: accelerated structure-based RNA virtual screening with deep graph learning.

Nature communications Mar 21, 2025
RNAs are a vast reservoir of untapped drug targets. Structure-based virtual screening (VS) identifies candidate molecules by leveraging binding site information, traditionally using molecular docking simulations. However, docking struggles to scale w...
Binding Sites Riboswitch RNA Nucleic Acid Conformation Molecular Docking Simulation Deep Learning
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RBPsuite 2.0: an updated RNA-protein binding site prediction suite with high coverage on species and proteins based on deep learning.

BMC biology Mar 11, 2025
BACKGROUND: RNA-binding proteins (RBPs) play crucial roles in many biological processes, and computationally identifying RNA-RBP interactions provides insights into the biological mechanism of diseases associated with RBPs.
RNA Binding Sites Computational Biology RNA-Binding Proteins RNA, Circular Software Deep Learning Humans
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DHUpredET: A comparative computational approach for identification of dihydrouridine modification sites in RNA sequence.

Analytical biochemistry Mar 6, 2025
Laboratory-based detection of D sites is laborious and expensive. In this study, we developed effective machine learning models employing efficient feature encoding methods to identify D sites. Initially, we explored various state-of-the-art feature ...
Machine Learning RNA Base Sequence Uridine Computational Biology Sequence Analysis, RNA
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RNA structure prediction using deep learning - A comprehensive review.

Computers in biology and medicine Feb 20, 2025
In computational biology, accurate RNA structure prediction offers several benefits, including facilitating a better understanding of RNA functions and RNA-based drug design. Implementing deep learning techniques for RNA structure prediction has led ...
Computational Biology RNA Humans Deep Learning Nucleic Acid Conformation
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RNA-protein interaction prediction using network-guided deep learning.

Communications biology Feb 16, 2025
Accurate computational determination of RNA-protein interactions remains challenging, particularly when encountering unknown RNAs and proteins. The limited number of RNAs and their flexibility constrained the effectiveness of the deep-learning models...
Humans Neural Networks, Computer SARS-CoV-2 Deep Learning COVID-19 RNA, Viral RNA Computational Biology RNA-Binding Proteins
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Identifying RNA-small Molecule Binding Sites Using Geometric Deep Learning with Language Models.

Journal of molecular biology Feb 15, 2025
RNAs are emerging as promising therapeutic targets, yet identifying small molecules that bind to them remains a significant challenge in drug discovery. This underscores the crucial role of computational modeling in predicting RNA-small molecule bind...
Binding Sites Small Molecule Libraries Deep Learning RNA Nucleic Acid Conformation Computational Biology Models, Molecular Drug Discovery
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