ArticleNucleic acids research2012
SETTER: web server for RNA structure comparison.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- ARTEM server: an online tool for nucleic acid 3D motif searches, 3D structure superposition and structure-based alignment.Nucleic acids research · 2026Article
- A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures.Nucleic acids research · 2023Article
- CircularSTAR3D: a stack-based RNA 3D structural alignment tool for circular matching.Nucleic acids research · 2023Article
- In silico optimization of RNA-protein interactions for CRISPR-Cas13-based antimicrobials.Biology direct · 2022Article
- Origin of the 16S Ribosomal Molecule from Ancestor tRNAs.Journal of molecular evolution · 2021Article
- LocalSTAR3D: a local stack-based RNA 3D structural alignment tool.Nucleic acids research · 2020Article
- RMalign: an RNA structural alignment tool based on a novel scoring function RMscore.BMC genomics · 2019Article
- Peptidyl Transferase Center and the Emergence of the Translation System.Life (Basel, Switzerland) · 2017Article
- RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation.BMC bioinformatics · 2017Article
- Topology independent comparison of RNA 3D structures using the CLICK algorithm.Nucleic acids research · 2017Article
- iPARTS2: an improved tool for pairwise alignment of RNA tertiary structures, version 2.Nucleic acids research · 2016Article
- The RNA 3D Motif Atlas: Computational methods for extraction, organization and evaluation of RNA motifs.Methods (San Diego, Calif.) · 2016Review
- MultiSETTER: web server for multiple RNA structure comparison.BMC bioinformatics · 2015Article
- RASS: a web server for RNA alignment in the joint sequence-structure space.Nucleic acids research · 2014Article
- R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.Nucleic acids research · 2013Article
- Analyzing and building nucleic acid structures with 3DNA.Journal of visualized experiments : JoVE · 2013Article
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3 authors.
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Abstract
The recent discoveries of regulatory non-coding RNAs changed our view of RNA as a simple information transfer molecule. Understanding the architecture and function of active RNA molecules requires methods for comparing and analyzing their 3D structures. While structural alignment of short RNAs is achievable in a reasonable amount of time, large structures represent much bigger challenge. Here, we present the SETTER web server for the RNA structure pairwise comparison utilizing the SETTER (SEcondary sTructure-based TERtiary Structure Similarity Algorithm) algorithm. The SETTER method divides an RNA structure into the set of non-overlapping structural elements called generalized secondary structure units (GSSUs). The SETTER algorithm scales as O(n(2)) with the size of a GSSUs and as O(n) with the number of GSSUs in the structure. This scaling gives SETTER its high speed as the average size of the GSSU remains constant irrespective of the size of the structure. However, the favorable speed of the algorithm does not compromise its accuracy. The SETTER web server together with the stand-alone implementation of the SETTER algorithm are freely accessible at http://siret.cz/setter.
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