AIMC Topic: Nucleic Acids

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Accurate structure prediction of biomolecular interactions with AlphaFold 3.

Nature
The introduction of AlphaFold 2 has spurred a revolution in modelling the structure of proteins and their interactions, enabling a huge range of applications in protein modelling and design. Here we describe our AlphaFold 3 model with a substantially...

DeePNAP: A Deep Learning Method to Predict Protein-Nucleic Acid Binding Affinity from Their Sequences.

Journal of chemical information and modeling
Predicting the protein-nucleic acid (PNA) binding affinity solely from their sequences is of paramount importance for the experimental design and analysis of PNA interactions (PNAIs). A large number of currently developed models for binding affinity ...

Mesophilic Argonaute-Mediated Polydisperse Droplet Biosensor for Amplification-Free, One-Pot, and Multiplexed Nucleic Acid Detection Using Deep Learning.

Analytical chemistry
Detection of nucleic acids from a single multiplexed and amplification-free test is critical for ensuring food safety, clinical diagnostics, and environmental monitoring. In this study, we introduced a mesophilic Argonaute protein from (CbAgo), whic...

Simple and Multiplexed Detection of Nucleic Acid Targets Based on Fluorescent Ring Patterns and Deep Learning Analysis.

ACS applied materials & interfaces
Simple diagnostic tests for nucleic acid targets can provide great advantages for applications such as rapid pathogen detection. Here, we developed a membrane assay for multiplexed detection of nucleic acid targets based on the visualization of two-d...

CryoREAD: de novo structure modeling for nucleic acids in cryo-EM maps using deep learning.

Nature methods
DNA and RNA play fundamental roles in various cellular processes, where their three-dimensional structures provide information critical to understanding the molecular mechanisms of their functions. Although an increasing number of nucleic acid struct...

Deep Learning Assisted Surface-Enhanced Raman Spectroscopy (SERS) for Rapid and Direct Nucleic Acid Amplification and Detection: Toward Enhanced Molecular Diagnostics.

ACS nano
Surface-enhanced Raman scattering (SERS) has evolved into a robust analytical technique capable of detecting a variety of biomolecules despite challenges in securing a reliable Raman signal. Conventional SERS-based nucleic acid detection relies on hy...

Structure-based prediction of nucleic acid binding residues by merging deep learning- and template-based approaches.

PLoS computational biology
Accurate prediction of nucleic binding residues is essential for the understanding of transcription and translation processes. Integration of feature- and template-based strategies could improve the prediction of these key residues in proteins. Never...

Programmable magnetic robot (ProMagBot) for automated nucleic acid extraction at the point of need.

Lab on a chip
Upstream sample preparation remains the bottleneck for point-of-need nucleic acid testing due to its complexity and time-consuming nature. Sample preparation involves extracting, purifying, and concentrating nucleic acids from various matrices. These...

Machine learning at the edge for AI-enabled multiplexed pathogen detection.

Scientific reports
Multiplexed detection of biomarkers in real-time is crucial for sensitive and accurate diagnosis at the point of use. This scenario poses tremendous challenges for detection and identification of signals of varying shape and quality at the edge of th...

A deep learning based method for automatic analysis of high-throughput droplet digital PCR images.

The Analyst
Droplet digital PCR (ddPCR) is a technique for absolute quantification of nucleic acid molecules and is widely used in biomedical research and clinical diagnosis. ddPCR partitions the reaction solution containing target molecules into a large number ...