RNApdbee

RNApdbee is a software tool that is designed to assist with the annotation of RNA structures, as well as the relationship between RNA's secondary and 3D structures. The tool is used in the field of RNA structural biology and bioinformatics, where having access to correctly annotated RNA structure is of crucial importance, especially in the secondary and 3D structure predictions. RNApdbee was introduced in 2014, and since then, it has been upgraded to RNApdbee 2.0, which is a highly advanced multifunctional tool with several features that make it stand out from its predecessor.

One of the most significant upgrades to RNApdbee 2.0 is the incorporation of new algorithms for recognition and classification of high-ordered pseudoknots in large RNA structures. This new feature allows for the analysis of isolated base pairs' impact on RNA structure and can visualize RNA secondary structures, including that of quadruplexes, with depiction of non-canonical interactions. Additionally, the software annotates motifs to ease the identification of stems, loops, and single-stranded fragments in the input RNA structure.

RNApdbee 2.0 is implemented as a publicly available webserver with an intuitive interface, which makes it accessible to anyone interested in using the software tool.

Topic

Nucleic acid structure analysis;Structure prediction;RNA;Protein secondary structure;Protein structural motifs and surfaces

Detail

  • Operation: RNA secondary structure prediction;Structure visualisation;RNA secondary structure alignment;RNA secondary structure analysis

  • Software interface: Web user interface

  • Language: Java

  • License: -

  • Cost: Free

  • Version name: 2.0

  • Credit: National Science Centre, Poland.

  • Input: PDB, PDBx/mmCIF, BPSEQ, CT

  • Output: -

  • Contact: -

  • Collection: -

  • Maturity: -

Publications

  • RNApdbee--a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs.
  • Antczak M, et al. RNApdbee--a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs. RNApdbee--a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs. 2014; 42:W368-72. doi: 10.1093/nar/gku330
  • https://doi.org/10.1093/nar/gku330
  • PMID: 24771339
  • PMC: PMC4086112
  • RNApdbee 2.0: multifunctional tool for RNA structure annotation.
  • Zok T, et al. RNApdbee 2.0: multifunctional tool for RNA structure annotation. RNApdbee 2.0: multifunctional tool for RNA structure annotation. 2018; 46:W30-W35. doi: 10.1093/nar/gky314
  • https://doi.org/10.1093/nar/gky314
  • PMID: 29718468
  • PMC: PMC6031003

Download and documentation

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