AIMC Topic: Nucleic Acid Conformation

Clear Filters Showing 21 to 30 of 121 articles

Critical Assessment of RNA and DNA Structure Predictions via Artificial Intelligence: The Imitation Game.

Journal of chemical information and modeling Mar 30, 2025
Computational predictions of biomolecular structure via artificial intelligence (AI) based approaches, as exemplified by AlphaFold software, have the potential to model of all life's biomolecules. We performed oligonucleotide structure prediction and...
Nucleic Acid Conformation Models, Molecular RNA Artificial Intelligence DNA
View on PubMed DOI

RNAmigos2: accelerated structure-based RNA virtual screening with deep graph learning.

Nature communications Mar 21, 2025
RNAs are a vast reservoir of untapped drug targets. Structure-based virtual screening (VS) identifies candidate molecules by leveraging binding site information, traditionally using molecular docking simulations. However, docking struggles to scale w...
Molecular Docking Simulation Nucleic Acid Conformation Binding Sites Riboswitch Deep Learning RNA
View on PubMed DOI

RNA structure prediction using deep learning - A comprehensive review.

Computers in biology and medicine Feb 20, 2025
In computational biology, accurate RNA structure prediction offers several benefits, including facilitating a better understanding of RNA functions and RNA-based drug design. Implementing deep learning techniques for RNA structure prediction has led ...
Nucleic Acid Conformation Computational Biology RNA Humans Deep Learning
View on PubMed DOI

Identifying RNA-small Molecule Binding Sites Using Geometric Deep Learning with Language Models.

Journal of molecular biology Feb 15, 2025
RNAs are emerging as promising therapeutic targets, yet identifying small molecules that bind to them remains a significant challenge in drug discovery. This underscores the crucial role of computational modeling in predicting RNA-small molecule bind...
Drug Discovery Models, Molecular RNA Nucleic Acid Conformation Deep Learning Computational Biology Binding Sites Small Molecule Libraries
View on PubMed DOI

Deep learning for RNA structure prediction.

Current opinion in structural biology Feb 10, 2025
Predicting RNA structures from sequences with computational approaches is of vital importance in RNA biology considering the high costs of experimental determination. AI methods have revolutionized this field in recent years, enabling RNA structure p...
RNA Nucleic Acid Conformation Deep Learning Computational Biology
View on PubMed DOI

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...
Genome Humans Deep Learning Nucleic Acid Conformation
View on PubMed DOI

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 Nucleic Acid Conformation DNA Silver Metal Nanoparticles Spectrum Analysis, Raman Citric Acid Support Vector Machine Discriminant Analysis
View on PubMed DOI

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...
Deep Learning Protein Binding RNA, Viral Molecular Dynamics Simulation Peptides RNA Nucleic Acid Conformation
View on PubMed DOI

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...
Chromatin Chromatin Immunoprecipitation Sequencing Nucleic Acid Conformation Regulatory Sequences, Nucleic Acid DNA Gene Expression Regulation Animals Single-Cell Analysis Humans Computational Biology Mice Machine Learning Transcription Factors
View on PubMed DOI

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...
RNA Sequence Analysis, RNA Deep Learning Sequence Alignment Nucleic Acid Conformation Benchmarking Computational Biology
View on PubMed DOI
Popular Topics
Recent Journals