AIMC Topic: Nucleic Acid Conformation

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Recipes and ingredients for deep learning models of 3D genome folding.

Current opinion in genetics & development Jan 24, 2025
Three-dimensional genome folding plays roles in gene regulation and disease. In this review, we compare and contrast recent deep learning models for predicting genome contact maps. We survey preprocessing, architecture, training, evaluation, and inte...
Nucleic Acid Conformation Genome Humans Deep Learning
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Advancing DNA Structural Analysis: A SERS Approach Free from Citrate Interference Combined with Machine Learning.

The journal of physical chemistry letters Jan 23, 2025
Surface-enhanced Raman spectroscopy (SERS) has become an indispensable tool for biomolecular analysis, yet the detection of DNA signals remains hindered by spectral interference from citrate ions, which overlap with key DNA features. This study intro...
Machine Learning Spectrum Analysis, Raman Support Vector Machine Discriminant Analysis Silver Citric Acid DNA Metal Nanoparticles Nucleic Acid Conformation
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Enhanced Sampling Simulations of RNA-Peptide Binding Using Deep Learning Collective Variables.

Journal of chemical information and modeling Jan 7, 2025
Enhanced sampling (ES) simulations of biomolecular recognition, such as binding small molecules to proteins and nucleic acid targets, protein-protein association, and protein-nucleic acid interactions, have gained significant attention in the simulat...
Molecular Dynamics Simulation RNA Nucleic Acid Conformation Deep Learning Protein Binding RNA, Viral Peptides
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ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning.

Nature communications Jan 2, 2025
Gene regulation is inherently multiscale, but scale-adaptive machine learning methods that fully exploit this property in single-nucleus accessibility data are still lacking. Here, we develop ChromatinHD, a pair of scale-adaptive models that uses the...
Mice Computational Biology Transcription Factors Animals Single-Cell Analysis Regulatory Sequences, Nucleic Acid Chromatin Chromatin Immunoprecipitation Sequencing Gene Expression Regulation Nucleic Acid Conformation DNA Humans Machine Learning
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Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction.

PLoS computational biology Dec 30, 2024
The 3D structure of RNA critically influences its functionality, and understanding this structure is vital for deciphering RNA biology. Experimental methods for determining RNA structures are labour-intensive, expensive, and time-consuming. Computati...
Deep Learning Computational Biology Benchmarking RNA Sequence Analysis, RNA Nucleic Acid Conformation Sequence Alignment
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Predicting RNA structure and dynamics with deep learning and solution scattering.

Biophysical journal Dec 25, 2024
Advanced deep learning and statistical methods can predict structural models for RNA molecules. However, RNAs are flexible, and it remains difficult to describe their macromolecular conformations in solutions where varying conditions can induce confo...
X-Ray Diffraction Nucleic Acid Conformation RNA Deep Learning Solutions Scattering, Small Angle Models, Molecular Magnesium
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Determining structures of RNA conformers using AFM and deep neural networks.

Nature Dec 18, 2024
Much of the human genome is transcribed into RNAs, many of which contain structural elements that are important for their function. Such RNA molecules-including those that are structured and well-folded-are conformationally heterogeneous and flexible...
Microscopy, Atomic Force Signal-To-Noise Ratio Nucleic Acid Conformation Unsupervised Machine Learning Humans Models, Molecular RNA Neural Networks, Computer Deep Learning
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Accurate RNA 3D structure prediction using a language model-based deep learning approach.

Nature methods Nov 21, 2024
Accurate prediction of RNA three-dimensional (3D) structures remains an unsolved challenge. Determining RNA 3D structures is crucial for understanding their functions and informing RNA-targeting drug development and synthetic biology design. The stru...
RNA Deep Learning Nucleic Acid Conformation Humans Computational Biology Software Models, Molecular
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Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21: A Machine-Learning-Aided Enhanced Sampling Study.

Journal of chemical information and modeling Nov 11, 2024
MicroRNAs (miRs) are short, noncoding RNA strands that regulate the activity of mRNAs by affecting the repression of protein translation, and their dysregulation has been implicated in several pathologies. miR21 in particular has been implicated in t...
Peptides, Cyclic Nucleic Acid Conformation RNA Precursors Molecular Dynamics Simulation Ribonuclease III Machine Learning Ligands Humans MicroRNAs
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Predicting synthetic mRNA stability using massively parallel kinetic measurements, biophysical modeling, and machine learning.

Nature communications Nov 6, 2024
mRNA degradation is a central process that affects all gene expression levels, though it remains challenging to predict the stability of a mRNA from its sequence, due to the many coupled interactions that control degradation rate. Here, we carried ou...
RNA, Bacterial Ribosomes RNA Stability Nucleic Acid Conformation Protein Biosynthesis RNA, Messenger Escherichia coli Kinetics Machine Learning
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