Machine learning modeling of RNA structures: methods, challenges and future perspectives
The three-dimensional structure of RNA molecules plays a critical role in a wide range of
cellular processes encompassing functions from riboswitches to epigenetic regulation …
cellular processes encompassing functions from riboswitches to epigenetic regulation …
Deep learning models for RNA secondary structure prediction (probably) do not generalize across families
Motivation The secondary structure of RNA is of importance to its function. Over the last few
years, several papers attempted to use machine learning to improve de novo RNA …
years, several papers attempted to use machine learning to improve de novo RNA …
[HTML][HTML] RNA3DB: A structurally-dissimilar dataset split for training and benchmarking deep learning models for RNA structure prediction
With advances in protein structure prediction thanks to deep learning models like AlphaFold,
RNA structure prediction has recently received increased attention from deep learning …
RNA structure prediction has recently received increased attention from deep learning …
Evaluating Performance of Different RNA Secondary Structure Prediction Programs Using Self-cleaving Ribozymes
Accurate identification of the correct, biologically relevant RNA structures is critical to
understanding various aspects of RNA biology since proper folding represents the key to …
understanding various aspects of RNA biology since proper folding represents the key to …
[HTML][HTML] CRPGCN: predicting circRNA-disease associations using graph convolutional network based on heterogeneous network
Z Ma, Z Kuang, L Deng - BMC bioinformatics, 2021 - Springer
Background The existing studies show that circRNAs can be used as a biomarker of
diseases and play a prominent role in the treatment and diagnosis of diseases. However …
diseases and play a prominent role in the treatment and diagnosis of diseases. However …
Res-Dom: predicting protein domain boundary from sequence using deep residual network and Bi-LSTM
L Wang, H Zhong, Z Xue, Y Wang - Bioinformatics Advances, 2022 - academic.oup.com
Motivation Protein domains are the basic units of proteins that can fold, function and evolve
independently. Protein domain boundary partition plays an important role in protein structure …
independently. Protein domain boundary partition plays an important role in protein structure …
SSCRB: Predicting circRNA-RBP interaction sites using a sequence and structural feature-based attention model
L Liu, Y Wei, Q Zhang, Q Zhao - IEEE Journal of Biomedical …, 2024 - ieeexplore.ieee.org
The prediction of interaction sites between circular RNA (circRNA) and RNA binding
proteins (RBPs) is crucial for regulating diseases and discovering new treatment …
proteins (RBPs) is crucial for regulating diseases and discovering new treatment …
[HTML][HTML] An Effective Deep Learning-Based Architecture for Prediction of N7-Methylguanosine Sites in Health Systems
N7-methylguanosine (m7G) is one of the most important epigenetic modifications found in
rRNA, mRNA, and tRNA, and performs a promising role in gene expression regulation …
rRNA, mRNA, and tRNA, and performs a promising role in gene expression regulation …
[HTML][HTML] Comparative analysis of RNA secondary structure accuracy on predicted RNA 3D models
RNA structure is conformationally dynamic, and accurate all-atom tertiary (3D) structure
modeling of RNA remains challenging with the prevailing tools. Secondary structure (2D) …
modeling of RNA remains challenging with the prevailing tools. Secondary structure (2D) …
[PDF][PDF] Computational Analysis of Codon Usage Bias, Single Nucleotide Polymorphism and RNA Secondary Structures in Microbial Genome Sequences
P Sen - 2023 - agnee.tezu.ernet.in
The majority of the genetic information of an organism is stored in the form of
Deoxyribonucleic acid (DNA) sequences bundled into one or more chromosomes. DNA …
Deoxyribonucleic acid (DNA) sequences bundled into one or more chromosomes. DNA …