ArticleComputational and structural biotechnology journal2020
3dRNA: Building RNA 3D structure with improved template library.
Article in Computational and structural biotechnology journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Cyclic transformation of stable/metastable nucleic acid structures enables dynamic monitoring of ATP in living cells.Chemical science · 2026Article
- RNAbpFlow: base pair-augmented SE(3) flow matching for conditional RNA 3D structure generation.Nature methods · 2026Article
- Single DNA hairpin nanowire based on self-hybridization chain reaction for sensitive ATP detection.Science and technology of advanced materials · 2026Article
- Challenges and opportunities in technologies and methods for lncRNA structure determination.Cell & bioscience · 2025Review
- Hsa_circ_0026782 Acts as a "Molecular Break" of CREB1-Mediated Transcription by Promoting Its Phosphorylation at Ser142 That Prevents Keloid Progression.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Phosphorylation Changes SARS-CoV-2 Nucleocapsid Protein's Structural Dynamics and Its Interaction With RNA.Proteins · 2025Article
- Advances in Protein-RNA aptamer recognition and modeling: Current trends and future perspectives.Current opinion in structural biology · 2025Review
- RNAbpFlow: Base pair-augmented SE(3)-flow matching for conditional RNA 3D structure generation.bioRxiv : the preprint server for biology · 2025Article
- Predicting RNA Structure Utilizing Attention from Pretrained Language Models.Journal of chemical information and modeling · 2025Article
- RNA-Puzzles Round V: blind predictions of 23 RNA structures.Nature methods · 2025Article
- Transformers in RNA structure prediction: A review.Computational and structural biotechnology journal · 2025Review
- IsRNAcirc: 3D structure prediction of circular RNAs based on coarse-grained molecular dynamics simulation.PLoS computational biology · 2024Article
- Comparative analysis of RNA 3D structure prediction methods: towards enhanced modeling of RNA-ligand interactions.Nucleic acids research · 2024Article
- State-of-the-RNArt: benchmarking current methods for RNA 3D structure prediction.NAR genomics and bioinformatics · 2024Article
- Prediction of 3D RNA Structures from Sequence Using Energy Landscapes of RNA Dimers: Application to RNA Tetraloops.Journal of chemical theory and computation · 2024Article
- Article
- Decoding the dual recognition mechanism of the glucocorticoid receptor for DNA and RNA: sequence versus shape.Scientific reports · 2023Article
- RNA 3D Structure Prediction: Progress and Perspective.Molecules (Basel, Switzerland) · 2023Review
- Role of RNA Domain Structure and Orientation in the Coxsackievirus B3 Virulence Phenotype.Journal of virology · 2023Article
- Directed Evolution of Seneca Valley Virus in Tumorsphere and Monolayer Cell Cultures of a Small-Cell Lung Cancer Model.Cancers · 2023Article
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Most of computational methods of building RNA tertiary structure are template-based. The template-based methods usually can give more accurate 3D structures due to the use of native 3D templates, but they cannot work if the 3D templates are not available. So, a more complete library of the native 3D templates is very important for this type of methods. 3dRNA is a template-based method for building RNA tertiary structure previously proposed by us. In this paper we report improved 3D template libraries of 3dRNA by using two different schemes that give two libraries 3dRNA_Lib1 and 3dRNA_Lib2. These libraries expand the original one by nearly ten times. Benchmark shows that they can significantly increase the accuracy of 3dRNA, especially in building complex and large RNA 3D structures.
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