AIMC Topic: RNA

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GenoM7GNet: An Efficient N-Methylguanosine Site Prediction Approach Based on a Nucleotide Language Model.

IEEE/ACM transactions on computational biology and bioinformatics Dec 10, 2024
N-methylguanosine (m7G), one of the mainstream post-transcriptional RNA modifications, occupies an exceedingly significant place in medical treatments. However, classic approaches for identifying m7G sites are costly both in time and equipment. Meanw...
Humans Neural Networks, Computer Algorithms Sequence Analysis, RNA RNA Guanosine Deep Learning Computational Biology
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Translation as a Biosignature.

Astrobiology Nov 29, 2024
Life on Earth relies on mechanisms to store heritable information and translate this information into cellular machinery required for biological activity. In all known life, storage, regulation, and translation are provided by DNA, RNA, and ribosomes...
Machine Learning DNA Protein Biosynthesis Ribosomes RNA Nanopores Exobiology
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Accurate RNA 3D structure prediction using a language model-based deep learning approach.

Nature methods Nov 21, 2024
Accurate prediction of RNA three-dimensional (3D) structures remains an unsolved challenge. Determining RNA 3D structures is crucial for understanding their functions and informing RNA-targeting drug development and synthetic biology design. The stru...
Computational Biology Models, Molecular Nucleic Acid Conformation RNA Humans Software Deep Learning
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Deciphering Cas9 specificity: Role of domain dynamics and RNA:DNA hybrid interactions revealed through machine learning and accelerated molecular simulations.

International journal of biological macromolecules Nov 19, 2024
CRISPR/Cas9 technology is widely used for gene editing, but off-targeting still remains a major concern in therapeutic applications. Although Cas9 variants with better mismatch discrimination have been developed, they have significantly lower rates o...
Molecular Dynamics Simulation RNA CRISPR-Associated Protein 9 Francisella Substrate Specificity Bacterial Proteins Protein Domains DNA CRISPR-Cas Systems Machine Learning
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Deep-m5U: a deep learning-based approach for RNA 5-methyluridine modification prediction using optimized feature integration.

BMC bioinformatics Nov 19, 2024
BACKGROUND: RNA 5-methyluridine (m5U) modifications play a crucial role in biological processes, making their accurate identification a key focus in computational biology. This paper introduces Deep-m5U, a robust predictor designed to enhance the pre...
Deep Learning Computational Biology RNA, Messenger Neural Networks, Computer Algorithms RNA Uridine
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Deep generative design of RNA aptamers using structural predictions.

Nature computational science Nov 6, 2024
RNAs represent a class of programmable biomolecules capable of performing diverse biological functions. Recent studies have developed accurate RNA three-dimensional structure prediction methods, which may enable new RNAs to be designed in a structure...
Computer Simulation Deep Learning Aptamers, Nucleotide Nucleic Acid Conformation Computational Biology RNA
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GeoNet enables the accurate prediction of protein-ligand binding sites through interpretable geometric deep learning.

Structure (London, England : 1993) Nov 1, 2024
The identification of protein binding residues is essential for understanding their functions in vivo. However, it remains a computational challenge to accurately identify binding sites due to the lack of known residue binding patterns. Local residue...
Ligands Binding Sites Computational Biology Proteins Models, Molecular RNA Deep Learning DNA Protein Binding
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PseU-KeMRF: A Novel Method for Identifying RNA Pseudouridine Sites.

IEEE/ACM transactions on computational biology and bioinformatics Oct 9, 2024
Pseudouridine is a type of abundant RNA modification that is seen in many different animals and is crucial for a variety of biological functions. Accurately identifying pseudouridine sites within the RNA sequence is vital for the subsequent study of ...
RNA Saccharomyces cerevisiae Pseudouridine Sequence Analysis, RNA Animals Support Vector Machine Mice Computational Biology Humans Algorithms
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Predicting RNA sequence-structure likelihood via structure-aware deep learning.

BMC bioinformatics Sep 30, 2024
BACKGROUND: The active functionalities of RNA are recognized to be heavily dependent on the structure and sequence. Therefore, a model that can accurately evaluate a design by giving RNA sequence-structure pairs would be a valuable tool for many rese...
RNA Computational Biology Nucleic Acid Conformation Neural Networks, Computer Sequence Analysis, RNA Deep Learning
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Capture of RNA-binding proteins across mouse tissues using HARD-AP.

Nature communications Sep 28, 2024
RNA-binding proteins (RBPs) modulate all aspects of RNA metabolism, but a comprehensive picture of RBP expression across tissues is lacking. Here, we describe our development of the method we call HARD-AP that robustly retrieves RBPs and tightly asso...
RNA-Binding Proteins RNA Binding Sites Protein Binding Machine Learning Humans Mice Animals
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