AIMC Topic: Nucleic Acid Conformation

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NucleoFind: a deep-learning network for interpreting nucleic acid electron density.

Nucleic acids research Sep 23, 2024
Nucleic acid electron density interpretation after phasing by molecular replacement or other methods remains a difficult problem for computer programs to deal with. Programs tend to rely on time-consuming and computationally exhaustive searches to re...
Software Deep Learning Nucleic Acids Crystallography, X-Ray Nucleic Acid Conformation Models, Molecular Electrons
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Advancing mRNA subcellular localization prediction with graph neural network and RNA structure.

Bioinformatics (Oxford, England) Aug 2, 2024
MOTIVATION: The asymmetrical distribution of expressed mRNAs tightly controls the precise synthesis of proteins within human cells. This non-uniform distribution, a cornerstone of developmental biology, plays a pivotal role in numerous cellular proce...
RNA, Messenger Nucleic Acid Conformation Humans Neural Networks, Computer Deep Learning Computational Biology Software
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Comparative analysis of RNA 3D structure prediction methods: towards enhanced modeling of RNA-ligand interactions.

Nucleic acids research Jul 22, 2024
Accurate RNA structure models are crucial for designing small molecule ligands that modulate their functions. This study assesses six standalone RNA 3D structure prediction methods-DeepFoldRNA, RhoFold, BRiQ, FARFAR2, SimRNA and Vfold2, excluding web...
Software Models, Molecular RNA Machine Learning Binding Sites Ligands RNA Folding Nucleic Acid Conformation
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sincFold: end-to-end learning of short- and long-range interactions in RNA secondary structure.

Briefings in bioinformatics May 23, 2024
MOTIVATION: Coding and noncoding RNA molecules participate in many important biological processes. Noncoding RNAs fold into well-defined secondary structures to exert their functions. However, the computational prediction of the secondary structure f...
RNA Nucleic Acid Conformation Deep Learning Computational Biology Thermodynamics Neural Networks, Computer Algorithms
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UFold: fast and accurate RNA secondary structure prediction with deep learning.

Nucleic acids research Feb 22, 2022
For many RNA molecules, the secondary structure is essential for the correct function of the RNA. Predicting RNA secondary structure from nucleotide sequences is a long-standing problem in genomics, but the prediction performance has reached a platea...
RNA Nucleic Acid Conformation Base Pairing Algorithms Deep Learning Humans
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CoCoNet-boosting RNA contact prediction by convolutional neural networks.

Nucleic acids research Dec 16, 2021
Co-evolutionary models such as direct coupling analysis (DCA) in combination with machine learning (ML) techniques based on deep neural networks are able to predict accurate protein contact or distance maps. Such information can be used as constraint...
Neural Networks, Computer Riboswitch Algorithms RNA Nucleic Acid Conformation Models, Molecular
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Geometric deep learning of RNA structure.

Science (New York, N.Y.) Aug 27, 2021
RNA molecules adopt three-dimensional structures that are critical to their function and of interest in drug discovery. Few RNA structures are known, however, and predicting them computationally has proven challenging. We introduce a machine learning...
Neural Networks, Computer RNA Deep Learning Nucleic Acid Conformation Models, Molecular
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Optical microlever assisted DNA stretching.

Optics express Aug 2, 2021
Optical microrobotics is an emerging field that has the potential to improve upon current optical tweezer studies through avenues such as limiting the exposure of biological molecules of interest to laser radiation and overcoming the current limitati...
Proof of Concept Study Nucleic Acid Conformation Optical Tweezers Optics and Photonics Robotics DNA
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Deep forest ensemble learning for classification of alignments of non-coding RNA sequences based on multi-view structure representations.

Briefings in bioinformatics Jul 20, 2021
Non-coding RNAs (ncRNAs) play crucial roles in multiple biological processes. However, only a few ncRNAs' functions have been well studied. Given the significance of ncRNAs classification for understanding ncRNAs' functions, more and more computation...
RNA, Untranslated Sequence Alignment Neural Networks, Computer Software Nucleic Acid Conformation
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DeepCLIP: predicting the effect of mutations on protein-RNA binding with deep learning.

Nucleic acids research Jul 27, 2020
Nucleotide variants can cause functional changes by altering protein-RNA binding in various ways that are not easy to predict. This can affect processes such as splicing, nuclear shuttling, and stability of the transcript. Therefore, correct modeling...
Base Sequence Protein Binding Nucleic Acid Conformation Mice Mutation Binding Sites Computational Biology RNA Nucleotide Motifs RNA-Binding Proteins Humans Animals Computer Simulation Deep Learning
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