AIMC Topic: Base Pairing

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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...
Deep Learning Base Pairing Nucleotide Motifs Thermodynamics Computational Biology RNA Nucleic Acid Conformation
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Electronic and Nuclear Quantum Effects on Proton Transfer Reactions of Guanine-Thymine (G-T) Mispairs Using Combined Quantum Mechanical/Molecular Mechanical and Machine Learning Potentials.

Molecules (Basel, Switzerland) Jun 6, 2024
Rare tautomeric forms of nucleobases can lead to Watson-Crick-like (WC-like) mispairs in DNA, but the process of proton transfer is fast and difficult to detect experimentally. NMR studies show evidence for the existence of short-time WC-like guanine...
Protons Machine Learning Thymine DNA Base Pairing Molecular Dynamics Simulation Thermodynamics Quantum Theory Guanine
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Predicting RNA secondary structure by a neural network: what features may be learned?

PeerJ Dec 13, 2022
Deep learning is a class of machine learning techniques capable of creating internal representation of data without explicit preprogramming. Hence, in addition to practical applications, it is of interest to analyze what features of biological data m...
Base Pairing Machine Learning Nucleotides RNA Humans Neural Networks, Computer
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Biological features between miRNAs and their targets are unveiled from deep learning models.

Scientific reports Dec 10, 2021
MicroRNAs (miRNAs) are ~ 22 nucleotide ubiquitous gene regulators. They modulate a broad range of essential cellular processes linked to human health and diseases. Consequently, identifying miRNA targets and understanding how they function are critic...
Computational Biology RNA, Messenger MicroRNAs Deep Learning Gene Regulatory Networks Base Pairing Databases, Nucleic Acid RNA Interference Models, Biological Gene Expression Regulation Mutagenesis Humans Algorithms
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Predicting base editing outcomes with an attention-based deep learning algorithm trained on high-throughput target library screens.

Nature communications Aug 25, 2021
Base editors are chimeric ribonucleoprotein complexes consisting of a DNA-targeting CRISPR-Cas module and a single-stranded DNA deaminase. They enable transition of C•G into T•A base pairs and vice versa on genomic DNA. While base editors have great ...
Gene Editing Base Pairing Gene Library Genome Algorithms Deep Learning High-Throughput Nucleotide Sequencing Humans
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Predicting the DNA Conductance Using a Deep Feedforward Neural Network Model.

Journal of chemical information and modeling Dec 15, 2020
Double-stranded DNA (dsDNA) has been established as an efficient medium for charge migration, bringing it to the forefront of the field of molecular electronics and biological research. The charge migration rate is controlled by the electronic coupli...
Base Pairing Neural Networks, Computer Machine Learning DNA Electronics
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Fast and accurate microRNA search using CNN.

BMC bioinformatics Dec 27, 2019
BACKGROUND: There are many different types of microRNAs (miRNAs) and elucidating their functions is still under intensive research. A fundamental step in functional annotation of a new miRNA is to classify it into characterized miRNA families, such a...
Neural Networks, Computer Algorithms MicroRNAs Probability Base Sequence RNA, Transfer Base Pairing Nucleotide Motifs
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Predicting RNA secondary structure via adaptive deep recurrent neural networks with energy-based filter.

BMC bioinformatics Dec 24, 2019
BACKGROUND: RNA secondary structure prediction is an important issue in structural bioinformatics, and RNA pseudoknotted secondary structure prediction represents an NP-hard problem. Recently, many different machine-learning methods, Markov models, a...
Base Pairing Neural Networks, Computer Thermodynamics RNA Nucleic Acid Conformation
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RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning.

Nature communications Nov 27, 2019
The majority of our human genome transcribes into noncoding RNAs with unknown structures and functions. Obtaining functional clues for noncoding RNAs requires accurate base-pairing or secondary-structure prediction. However, the performance of such p...
Base Pairing RNA, Untranslated Protein Structure, Secondary Databases, Genetic RNA Algorithms Deep Learning Humans Computational Biology Neural Networks, Computer Software
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Integrating DNA structure switch with branched hairpins for the detection of uracil-DNA glycosylase activity and inhibitor screening.

Talanta Nov 22, 2017
The detection of uracil-DNA glycosylase (UDG) activity is pivotal for its biochemical studies and the development of drugs for UDG-related diseases. Here, we explored an integrated DNA structure switch for high sensitive detection of UDG activity. Th...
G-Quadruplexes Base Pairing DNA Humans Inverted Repeat Sequences Fluorescent Dyes MCF-7 Cells Limit of Detection Benzothiazoles Oligonucleotides Spectrometry, Fluorescence High-Throughput Screening Assays Uracil-DNA Glycosidase HeLa Cells Thiazoles Enzyme Inhibitors
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