AIMC Topic: DNA

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Autonomous assembly and disassembly of gliding molecular robots regulated by a DNA-based molecular controller.

Science advances May 31, 2024
In recent years, there has been a growing interest in engineering dynamic and autonomous systems with robotic functionalities using biomolecules. Specifically, the ability of molecular motors to convert chemical energy to mechanical forces and the pr...
Molecular Motor Proteins Kinesins Robotics DNA Microtubules
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Prediction of Protein-DNA Interface Hot Spots Based on Empirical Mode Decomposition and Machine Learning.

Genes May 23, 2024
Protein-DNA complex interactivity plays a crucial role in biological activities such as gene expression, modification, replication and transcription. Understanding the physiological significance of protein-DNA binding interfacial hot spots, as well a...
Protein Binding Computational Biology DNA Machine Learning Algorithms DNA-Binding Proteins Binding Sites
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Predicting Serotonin Detection with DNA-Carbon Nanotube Sensors across Multiple Spectral Wavelengths.

Journal of chemical information and modeling May 13, 2024
Owing to the value of DNA-wrapped single-walled carbon nanotube (SWNT)-based sensors for chemically specific imaging in biology, we explore machine learning (ML) predictions DNA-SWNT serotonin sensor responsivity as a function of DNA sequence based o...
Machine Learning Nanotubes, Carbon Base Sequence DNA Biosensing Techniques Spectrometry, Fluorescence Serotonin
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Prediction of Transcription Factor Binding Sites on Cell-Free DNA Based on Deep Learning.

Journal of chemical information and modeling May 9, 2024
Transcription factors (TFs) are important regulatory elements for vital cellular activities, and the identification of transcription factor binding sites (TFBS) can help to explore gene regulatory mechanisms. Research studies have proved that cfDNA (...
Binding Sites Cell-Free Nucleic Acids DNA Deep Learning Humans Transcription Factors
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Discrimination of Genetic Biomarkers of Disease through Machine-Learning-Based Hypothesis Testing of Direct SERS Spectra of DNA and RNA.

ACS sensors Apr 29, 2024
Cancer is globally a leading cause of death that would benefit from diagnostic approaches detecting it in its early stages. However, despite much research and investment, cancer early diagnosis is still underdeveloped. Owing to its high sensitivity, ...
DNA DNA, Single-Stranded Metal Nanoparticles Genetic Markers Spectrum Analysis, Raman Silver Humans RNA MicroRNAs Machine Learning
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Generalized biomolecular modeling and design with RoseTTAFold All-Atom.

Science (New York, N.Y.) Apr 19, 2024
Deep-learning methods have revolutionized protein structure prediction and design but are presently limited to protein-only systems. We describe RoseTTAFold All-Atom (RFAA), which combines a residue-based representation of amino acids and DNA bases w...
Amino Acids Protein Engineering Crystallography DNA Models, Molecular Deep Learning Proteins
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DNA shape features improve prediction of CRISPR/Cas9 activity.

Methods (San Diego, Calif.) Apr 17, 2024
The CRISPR/Cas9 genome editing technology has transformed basic and translational research in biology and medicine. However, the advances are hindered by off-target effects and a paucity in the knowledge of the mechanism of the Cas9 protein. Machine ...
Neural Networks, Computer Machine Learning Epigenesis, Genetic Gene Editing Humans DNA Bayes Theorem Nucleic Acid Conformation CRISPR-Cas Systems
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A novel activation function based on DNA enzyme-free hybridization reaction and its implementation on nonlinear molecular learning systems.

Physical chemistry chemical physics : PCCP Apr 17, 2024
With the advent of the post-Moore's Law era, the development of traditional silicon-based computers has reached its limit, and there is an urgent need to develop new computing technologies to meet the needs of science, technology, and daily life. Due...
Computers DNA Computers, Molecular Neural Networks, Computer Artificial Intelligence Humans
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ESPDHot: An Effective Machine Learning-Based Approach for Predicting Protein-DNA Interaction Hotspots.

Journal of chemical information and modeling Apr 8, 2024
Protein-DNA interactions are pivotal to various cellular processes. Precise identification of the hotspot residues for protein-DNA interactions holds great significance for revealing the intricate mechanisms in protein-DNA recognition and for providi...
Thermodynamics Protein Binding Support Vector Machine Neural Networks, Computer DNA Proteins Machine Learning DNA-Binding Proteins Algorithms
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Boosting Clear Cell Renal Carcinoma-Specific Drug Discovery Using a Deep Learning Algorithm and Single-Cell Analysis.

International journal of molecular sciences Apr 8, 2024
Clear cell renal carcinoma (ccRCC), the most common subtype of renal cell carcinoma, has the high heterogeneity of a highly complex tumor microenvironment. Existing clinical intervention strategies, such as target therapy and immunotherapy, have fail...
Single-Cell Analysis DNA Kidney Neoplasms Endothelial Cells DNA Modification Methylases Tumor Microenvironment Drug Discovery Deep Learning Humans Algorithms Carcinoma, Renal Cell Antimetabolites
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