AIMC Topic: Nucleic Acid Conformation

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Sensitive detection of DNA methyltransferase using the dendritic rolling circle amplification-induced fluorescence.

Analytica chimica acta Dec 27, 2016
The analysis of DNA methylation and MTase activities is very important in the early clinical diagnosis of cancer, on purposes of providing insights into the mechanism of gene repression and developing novel drugs of treating methylation-related disea...
DNA Probes Nucleic Acid Conformation DNA, Catalytic DNA Methylation Nucleic Acid Amplification Techniques DNA Modification Methylases Fluorescence
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A Machine Learning Approach for MicroRNA Precursor Prediction in Retro-transcribing Virus Genomes.

Journal of integrative bioinformatics Dec 22, 2016
Identification of microRNA (miRNA) precursors has seen increased efforts in recent years. The difficulty in experimental detection of pre-miRNAs increased the usage of computational approaches. Most of these approaches rely on machine learning especi...
ROC Curve Nucleic Acid Conformation Genome, Viral Humans MicroRNAs RNA Precursors Artificial Intelligence Reverse Transcription Genome, Human
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Mirnacle: machine learning with SMOTE and random forest for improving selectivity in pre-miRNA ab initio prediction.

BMC bioinformatics Dec 15, 2016
BACKGROUND: MicroRNAs (miRNAs) are key gene expression regulators in plants and animals. Therefore, miRNAs are involved in several biological processes, making the study of these molecules one of the most relevant topics of molecular biology nowadays...
Computer Simulation Animals Genomics Humans Genome Plants Machine Learning Nucleic Acid Conformation Eukaryota Computational Biology MicroRNAs
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LBSizeCleav: improved support vector machine (SVM)-based prediction of Dicer cleavage sites using loop/bulge length.

BMC bioinformatics Nov 25, 2016
BACKGROUND: Dicer is necessary for the process of mature microRNA (miRNA) formation because the Dicer enzyme cleaves pre-miRNA correctly to generate miRNA with correct seed regions. Nonetheless, the mechanism underlying the selection of a Dicer cleav...
Algorithms Support Vector Machine MicroRNAs Humans Software Nucleic Acid Conformation RNA Precursors DEAD-box RNA Helicases Bayes Theorem Base Sequence Ribonuclease III
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A semi-supervised learning approach for RNA secondary structure prediction.

Computational biology and chemistry Feb 20, 2015
RNA secondary structure prediction is a key technology in RNA bioinformatics. Most algorithms for RNA secondary structure prediction use probabilistic models, in which the model parameters are trained with reliable RNA secondary structures. Because o...
Supervised Machine Learning Nucleic Acid Conformation Stochastic Processes RNA
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Identifying DNA-binding proteins by combining support vector machine and PSSM distance transformation.

BMC systems biology Feb 6, 2015
BACKGROUND: DNA-binding proteins play a pivotal role in various intra- and extra-cellular activities ranging from DNA replication to gene expression control. Identification of DNA-binding proteins is one of the major challenges in the field of genome...
Sequence Analysis, Protein Nucleic Acid Conformation Molecular Sequence Data Amino Acid Sequence Protein Conformation Computational Biology Support Vector Machine Internet DNA-Binding Proteins Models, Molecular
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Machine Learning-Augmented Molecular Dynamics Simulations (MD) Reveal Insights Into the Disconnect Between Affinity and Activation of ZTP Riboswitch Ligands.

Angewandte Chemie (International ed. in English) Jul 28, 2025
The challenge of targeting RNA with small molecules necessitates a better understanding of RNA-ligand interaction mechanisms. However, the dynamic nature of nucleic acids, their ligand-induced stabilization, and how conformational changes influence g...
Machine Learning Molecular Dynamics Simulation Ribonucleotides Riboswitch Aminoimidazole Carboxamide Ligands Nucleic Acid Conformation
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Characterizing DNA Origami Nanostructures in TEM Images Using Convolutional Neural Networks.

Journal of chemical information and modeling Jul 14, 2025
Artificial intelligence (AI) models remain an emerging strategy to accelerate materials design and development. We demonstrate that CNN models can characterize DNA origami nanostructures employed in programmable self-assembly, which is important in m...
Nanostructures Nucleic Acid Conformation Microscopy, Electron, Transmission DNA Convolutional Neural Networks Molecular Dynamics Simulation Neural Networks, Computer Image Processing, Computer-Assisted
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A Hyperbolic Discrete Diffusion 3D RNA Inverse Folding Model for Functional RNA Design.

Journal of chemical information and modeling Jul 14, 2025
Generative design of functional RNAs presents revolutionary opportunities for diverse RNA-based biotechnologies and biomedical applications. To this end, RNA inverse folding is a promising strategy for generatively designing new RNA sequences that ca...
Nucleic Acid Conformation Models, Molecular RNA Folding Diffusion RNA Deep Learning
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Predicting rare DNA conformations via dynamical graphical models: a case study of the B→A transition.

Nucleic acids research Jul 8, 2025
DNA exhibits local conformational preferences that affect its ability to adopt biologically relevant conformations, such as those required for binding proteins. Traditional methods, like Markov state models and molecular dynamics (MD) simulations, ha...
Molecular Dynamics Simulation Nucleic Acid Conformation Thermodynamics Machine Learning DNA
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