Results 1 to 10 of about 9,562,225 (293)
Transformers in RNA structure prediction: A review [PDF]
Computational and Structural Biotechnology JournalThe Transformer is a deep neural network based on the self-attention mechanism, designed to handle sequential data. Given its tremendous advantages in natural language processing, it has gained traction for other applications. As the primary structure of
Mayank Chaturvedi +2 more
doaj +6 more sources
RNA 3D Structure Prediction: Progress and Perspective
Molecules, 2023 Ribonucleic acid (RNA) molecules play vital roles in numerous important biological functions such as catalysis and gene regulation. The functions of RNAs are strongly coupled to their structures or proper structure changes, and RNA structure prediction ...
Xunxun Wang +4 more
doaj +4 more sources
Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction. [PDF]
PLoS Computational BiologyThe 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. Computational
Akash Bahai +3 more
doaj +2 more sources
RNA secondary structure prediction with pseudoknots: Contribution of algorithm versus energy model. [PDF]
PLoS ONE, 2018 RNA is a biopolymer with various applications inside the cell and in biotechnology. Structure of an RNA molecule mainly determines its function and is essential to guide nanostructure design.
Hosna Jabbari +2 more
doaj +3 more sources
Review of machine learning methods for RNA secondary structure prediction.
PLoS Computational Biology, 2021 Secondary structure plays an important role in determining the function of noncoding RNAs. Hence, identifying RNA secondary structures is of great value to research. Computational prediction is a mainstream approach for predicting RNA secondary structure.
Qi Zhao +5 more
doaj +2 more sources
DRfold2 is a deep learning-based tool that enables efficient and accurate RNA structure prediction. [PDF]
PLoS BiologyRNA structures are essential for understanding their biological functions and developing RNA-targeted therapeutics. However, accurate RNA structure prediction from sequence remains a crucial challenge. We introduce DRfold2, a deep learning framework that
Yang Li +5 more
doaj +2 more sources
Comparative analysis of RNA secondary structure accuracy on predicted RNA 3D models
PLoS ONE, 2023 RNA structure is conformationally dynamic, and accurate all-atom tertiary (3D) structure modeling of RNA remains challenging with the prevailing tools. Secondary structure (2D) information is the standard prerequisite for most RNA 3D modeling.
Mandar Kulkarni +3 more
doaj +3 more sources
RNA Biology, 2023 CRISPR technologies comprising a Cas nuclease and a guide RNA (gRNA) can utilize multiple gRNAs to enact multi-site editing or regulation in the same cell.
Sandra Gawlitt +3 more
doaj +1 more source
IndelsRNAmute: predicting deleterious multiple point substitutions and indels mutations
BMC Bioinformatics, 2022 Background RNA deleterious point mutation prediction was previously addressed with programs such as RNAmute and MultiRNAmute. The purpose of these programs is to predict a global conformational rearrangement of the secondary structure of a functional RNA
Alexander Churkin +2 more
doaj +1 more source
HiPR: High-throughput probabilistic RNA structure inference
Computational and Structural Biotechnology Journal, 2020 Recent high-throughput structure-sensitive genome-wide sequencing-based assays have enabled large-scale studies of RNA structure, and robust transcriptome-wide computational prediction of individual RNA structures across RNA classes from these assays has
Pavel P. Kuksa +5 more
doaj +1 more source