AIMC Topic: Aptamers, Nucleotide

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Machine learning guided aptamer refinement and discovery.

Nature communications Apr 22, 2021
Aptamers are single-stranded nucleic acid ligands that bind to target molecules with high affinity and specificity. They are typically discovered by searching large libraries for sequences with desirable binding properties. These libraries, however, ...
Protein Binding Models, Chemical Lipocalin-2 Ligands Gene Library Computer Simulation Drug Discovery Aptamers, Nucleotide Machine Learning
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A convolutional neural network for the prediction and forward design of ribozyme-based gene-control elements.

eLife Apr 16, 2021
Ribozyme switches are a class of RNA-encoded genetic switch that support conditional regulation of gene expression across diverse organisms. An improved elucidation of the relationships between sequence, structure, and activity can improve our capaci...
Models, Genetic Escherichia coli Structure-Activity Relationship Computer-Aided Design Aptamers, Nucleotide Sequence Analysis, RNA Base Sequence Nucleic Acid Conformation Saccharomyces cerevisiae RNA, Catalytic Ligands High-Throughput Nucleotide Sequencing Gene Expression Regulation Neural Networks, Computer Machine Learning
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AptaNet as a deep learning approach for aptamer-protein interaction prediction.

Scientific reports Mar 16, 2021
Aptamers are short oligonucleotides (DNA/RNA) or peptide molecules that can selectively bind to their specific targets with high specificity and affinity. As a powerful new class of amino acid ligands, aptamers have high potentials in biosensing, the...
Deep Learning Aptamers, Nucleotide Proteins Databases, Protein
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An apta-aggregation based machine learning assay for rapid quantification of lysozyme through texture parameters.

PloS one Mar 8, 2021
A novel assay technique that involves quantification of lysozyme (Lys) through machine learning is put forward here. This article reports the tendency of the well- documented Ellington group anti-Lys aptamer, to produce aggregates when exposed to Lys...
Aptamers, Nucleotide Chickens Avian Proteins Protein Aggregates Muramidase Machine Learning Animals
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In silico design of novel aptamers utilizing a hybrid method of machine learning and genetic algorithm.

Molecular diversity Feb 7, 2021
Aptamers can be regarded as efficient substitutes for monoclonal antibodies in many diagnostic and therapeutic applications. Due to the tedious and prohibitive nature of SELEX (systematic evolution of ligands by exponential enrichment), the in silico...
Drug Design Aptamers, Nucleotide Proteins Algorithms Biomarkers Molecular Docking Simulation Molecular Conformation CD13 Antigens Molecular Dynamics Simulation RNA Ligands Machine Learning
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Porphyrin-based covalent organic framework as bioplatfrom for detection of vascular endothelial growth factor 165 through fluorescence resonance energy transfer.

Talanta Dec 30, 2020
A fluorescent aptasensor based on porphyrin-based covalent organic framework (p-COF) and carbon dots (CDs) was constructed for detecting vascular endothelial growth factor 165 (VEGF) and for imaging of the breast cancer cell line Michigan cancer foun...
Porphyrins Vascular Endothelial Growth Factor A Fluorescence Resonance Energy Transfer Quantum Dots Humans Limit of Detection Aptamers, Nucleotide Metal-Organic Frameworks Biosensing Techniques
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Improved Antibiotic Detection in Raw Milk Using Machine Learning Tools over the Absorption Spectra of a Problem-Specific Nanobiosensor.

Sensors (Basel, Switzerland) Aug 14, 2020
In this article we present the development of a biosensor system that integrates nanotechnology, optomechanics and a spectral detection algorithm for sensitive quantification of antibiotic residues in raw milk of cow. Firstly, nanobiosensors were des...
Drug Residues Metal Nanoparticles Limit of Detection Milk Machine Learning Food Contamination Anti-Bacterial Agents Aptamers, Nucleotide Gold Animals Biosensing Techniques
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Aptamer based proteomic pilot study reveals a urine signature indicative of pediatric urinary tract infections.

PloS one Jul 6, 2020
OBJECTIVE: Current urinary tract infection (UTI) diagnostic strategies that rely on leukocyte esterase have limited accuracy. We performed an aptamer-based proteomics pilot study to identify urine protein levels that could differentiate a culture pro...
Urinary Tract Infections Aptamers, Nucleotide Biomarkers Adolescent Urinalysis Female Proteomics Male Child, Preschool Support Vector Machine Humans Pilot Projects Child Prospective Studies
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Design a fluorometric aptasensor based on CoOOH nanosheets and carbon dots for simultaneous detection of lysozyme and adenosine triphosphate.

Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy Feb 29, 2020
Simultaneous detection of biomarkers and biomolecules with great analytical performance still is challenging. A simple fluorometric dual-functional aptasensor was designed to detect Lysozyme (LYS) and adenosine triphosphate (ATP) as models of a prote...
Aptamers, Nucleotide Biosensing Techniques Support Vector Machine Quantum Dots Cobalt Spectrometry, Fluorescence Electronic Data Processing Oxides Muramidase Adenosine Triphosphate
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A generative model for constructing nucleic acid sequences binding to a protein.

BMC genomics Dec 27, 2019
BACKGROUND: Interactions between protein and nucleic acid molecules are essential to a variety of cellular processes. A large amount of interaction data generated by high-throughput technologies have triggered the development of several computational...
Proteins DNA Base Sequence Aptamers, Nucleotide Protein Binding Transcription Factors Humans Nucleic Acid Conformation Neural Networks, Computer Algorithms
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