AIMC Topic: Nucleic Acid Conformation

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Generative and predictive neural networks for the design of functional RNA molecules.

Nature communications May 4, 2025
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...
RNA Nucleic Acid Conformation Neural Networks, Computer Algorithms Thermodynamics
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GINClus: RNA structural motif clustering using graph isomorphism network.

NAR genomics and bioinformatics Apr 26, 2025
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...
Algorithms Deep Learning Software Nucleic Acid Conformation Nucleotide Motifs Cluster Analysis RNA
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A divide-and-conquer approach based on deep learning for long RNA secondary structure prediction: Focus on pseudoknots identification.

PloS one Apr 25, 2025
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...
Deep Learning Software Computational Biology Algorithms Nucleic Acid Conformation RNA, Long Noncoding RNA Folding RNA
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Identification of potential riboswitch elements in Homo sapiens mRNA 5'UTR sequences using positive-unlabeled machine learning.

PloS one Apr 24, 2025
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 ...
RNA, Messenger Ligands Riboswitch Humans Base Sequence 5' Untranslated Regions Machine Learning Nucleic Acid Conformation
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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 Computational Biology RNA Models, Molecular Ligands Deep Learning Nucleic Acid Conformation Binding Sites
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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...
RNA Nucleic Acid Conformation DNA Models, Molecular Artificial Intelligence
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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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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 ...
Nucleic Acid Conformation Computational Biology RNA Humans Deep Learning
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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...
Drug Discovery Deep Learning Computational Biology Small Molecule Libraries Nucleic Acid Conformation Models, Molecular Binding Sites RNA
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Deep learning for RNA structure prediction.

Current opinion in structural biology Feb 10, 2025
Predicting RNA structures from sequences with computational approaches is of vital importance in RNA biology considering the high costs of experimental determination. AI methods have revolutionized this field in recent years, enabling RNA structure p...
Nucleic Acid Conformation Deep Learning Computational Biology RNA
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