ArticleNucleic acids research2014
RNApdbee--a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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47 citing papers in PubMed.
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- PseudoknotVisualizer: Visualization of pseudoknots on three-dimensional RNA structures.PLoS computational biology · 2025Article
- Cryo-EM structure of ribosome from pathogenic protozoa Entamoeba histolytica reveals unique features of its architecture.Nature communications · 2025Article
- TARNAS: A Software Tool for Abstracting and Translating RNA Secondary Structures.International journal of molecular sciences · 2025Article
- Dissecting the Conformational Heterogeneity of Stem-Loop Substructures of the Fifth Element in the 5'-Untranslated Region of SARS-CoV-2.Journal of the American Chemical Society · 2024Article
- Advancing RNA 3D structure prediction: Exploring hierarchical and hybrid approaches in CASP15.Proteins · 2023Article
- The structure of a hibernating ribosome in a Lyme disease pathogen.Nature communications · 2023Article
- Automatic generation of pseudoknotted RNAs taxonomy.BMC bioinformatics · 2023Article
- Machine learning for RNA 2D structure prediction benchmarked on experimental data.Briefings in bioinformatics · 2023Review
- The assessment of molecular dynamics results of three-dimensional RNA aptamer structure prediction.PloS one · 2023Article
- Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models.International journal of molecular sciences · 2022Article
- Phenological segregation suggests speciation by time in the planktonic diatomEcology and evolution · 2022Article
- VfoldMCPX: predicting multistrand RNA complexes.RNA (New York, N.Y.) · 2022Article
- Bacterial 2'-Deoxyguanosine Riboswitch Classes as Potential Targets for Antibiotics: A Structure and Dynamics Study.International journal of molecular sciences · 2022Article
- Length-Dependent Deep Learning Model for RNA Secondary Structure Prediction.Molecules (Basel, Switzerland) · 2022Article
- Template switching in DNA replication can create and maintain RNA hairpins.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Nuclear and Mitochondrial SSU rRNA Genes Reveal Hidden Diversity ofFrontiers in microbiology · 2022Article
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Authors and funding
7 authors.
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Abstract
In RNA structural biology and bioinformatics an access to correct RNA secondary structure and its proper representation is of crucial importance. This is true especially in the field of secondary and 3D RNA structure prediction. Here, we introduce RNApdbee-a new tool that allows to extract RNA secondary structure from the pdb file, and presents it in both textual and graphical form. RNApdbee supports processing of knotted and unknotted structures of large RNAs, also within protein complexes. The method works not only for first but also for high order pseudoknots, and gives an information about canonical and non-canonical base pairs. A combination of these features is unique among existing applications for RNA structure analysis. Additionally, a function of converting between the text notations, i.e. BPSEQ, CT and extended dot-bracket, is provided. In order to facilitate a more comprehensive study, the webserver integrates the functionality of RNAView, MC-Annotate and 3DNA/DSSR, being the most common tools used for automated identification and classification of RNA base pairs. RNApdbee is implemented as a publicly available webserver with an intuitive interface and can be freely accessed at http://rnapdbee.cs.put.poznan.pl/.
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