AIMC Topic: Nucleic Acid Conformation

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Enzymatic Weight Update Algorithm for DNA-Based Molecular Learning.

Molecules (Basel, Switzerland) Apr 10, 2019
Recent research in DNA nanotechnology has demonstrated that biological substrates can be used for computing at a molecular level. However, in vitro demonstrations of DNA computations use preprogrammed, rule-based methods which lack the adaptability t...
DNA Models, Molecular Nucleic Acid Conformation Neural Networks, Computer Machine Learning
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Identification of D Modification Sites by Integrating Heterogeneous Features in .

Molecules (Basel, Switzerland) Jan 22, 2019
As an abundant post-transcriptional modification, dihydrouridine (D) has been found in transfer RNA (tRNA) from bacteria, eukaryotes, and archaea. Nonetheless, knowledge of the exact biochemical roles of dihydrouridine in mediating tRNA function is s...
Chemical Phenomena Nucleic Acid Conformation Saccharomyces cerevisiae RNA, Transfer Uridine Algorithms Reproducibility of Results Support Vector Machine
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Tuning the Performance of Synthetic Riboswitches using Machine Learning.

ACS synthetic biology Jan 8, 2019
Riboswitch development for clinical, technological, and synthetic biology applications constantly seeks to optimize regulatory behavior. Here, we present a machine learning approach to improve the regulation of a tetracycline (tc)-dependent riboswitc...
Machine Learning Synthetic Biology Aptamers, Nucleotide Nucleic Acid Conformation Riboswitch Computational Biology Tetracycline
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Rapid and specific detection of Salmonella infections using chemically modified nucleic acid probes.

Analytica chimica acta Dec 21, 2018
Salmonella is a leading source of bacterial foodborne illness in humans, causing gastroenteritis outbreaks with bacteraemia occurrences that can lead to clinical complications and death. Eggs, poultry and pig products are considered as the main carri...
Food Safety Deoxyribonucleases Protein Conformation Nucleic Acid Conformation Salmonella Oligonucleotide Probes Time Factors Food Microbiology Models, Molecular Limit of Detection
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Prediction of CRISPR sgRNA Activity Using a Deep Convolutional Neural Network.

Journal of chemical information and modeling Dec 7, 2018
The CRISPR-Cas9 system derived from adaptive immunity in bacteria and archaea has been developed into a powerful tool for genome engineering with wide-ranging applications. Optimizing single-guide RNA (sgRNA) design to improve efficiency of target cl...
Models, Molecular CRISPR-Cas Systems Gene Editing Deep Learning Computational Biology Nucleic Acid Conformation RNA, Guide, CRISPR-Cas Systems
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RNA3DCNN: Local and global quality assessments of RNA 3D structures using 3D deep convolutional neural networks.

PLoS computational biology Nov 27, 2018
Quality assessment is essential for the computational prediction and design of RNA tertiary structures. To date, several knowledge-based statistical potentials have been proposed and proved to be effective in identifying native and near-native RNA st...
Datasets as Topic Hot Temperature Nucleic Acid Conformation Molecular Dynamics Simulation RNA Monte Carlo Method Neural Networks, Computer
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Prediction of RNA-protein sequence and structure binding preferences using deep convolutional and recurrent neural networks.

BMC genomics Jul 3, 2018
BACKGROUND: RNA regulation is significantly dependent on its binding protein partner, known as the RNA-binding proteins (RBPs). Unfortunately, the binding preferences for most RBPs are still not well characterized. Interdependencies between sequence ...
RNA Nucleic Acid Conformation Binding Sites Nucleotide Motifs Protein Binding Computational Biology RNA-Binding Proteins Algorithms User-Computer Interface Neural Networks, Computer
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DPP-PseAAC: A DNA-binding protein prediction model using Chou's general PseAAC.

Journal of theoretical biology May 16, 2018
A DNA-binding protein (DNA-BP) is a protein that can bind and interact with a DNA. Identification of DNA-BPs using experimental methods is expensive as well as time consuming. As such, fast and accurate computational methods are sought for predicting...
Algorithms Reproducibility of Results Protein Domains Amino Acids DNA-Binding Proteins Amino Acid Sequence Nucleic Acid Conformation Databases, Protein Computational Biology DNA Support Vector Machine Models, Molecular
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The first two mitochondrial genomes from Taeniopterygidae (Insecta: Plecoptera): Structural features and phylogenetic implications.

International journal of biological macromolecules Dec 29, 2017
The complete mitochondrial genomes (mitogenomes) of Taeniopteryx ugola and Doddsia occidentalis (Plecoptera: Taeniopterygidae) were firstly sequenced from the family Taeniopterygidae. The 15,353-bp long mitogenome of T. ugola and the 16,020-bp long m...
Whole Genome Sequencing Nucleic Acid Conformation RNA, Transfer Animals Phylogeny Genome, Mitochondrial Lepidoptera RNA, Ribosomal
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DotAligner: identification and clustering of RNA structure motifs.

Genome biology Dec 28, 2017
The diversity of processed transcripts in eukaryotic genomes poses a challenge for the classification of their biological functions. Sparse sequence conservation in non-coding sequences and the unreliable nature of RNA structure predictions further e...
Nucleic Acid Conformation Nucleotide Motifs RNA, Untranslated Cluster Analysis Algorithms RNA Reproducibility of Results Base Sequence Computational Biology Genomics RNA-Binding Proteins
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