About: Efficient RNA pairwise structure comparison by SETTER method

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An Entity of Type : http://linked.opendata.cz/ontology/domain/vavai/Vysledek, within Data Space : linked.opendata.cz associated with source document(s)

Attributes	Values
rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
rdfs:seeAlso	http://dx.doi.org/10.1093/bioinformatics/bts301
Description	Motivation: Understanding the architecture and function of RNA molecules requires methods for comparing and analyzing their 3D structures. Although a structural alignment of short RNAs is achievable in a reasonable amount of time, large structures represent much bigger challenge. However, the growth of the number of large RNAs deposited in the PDB database calls for the development of fast and accurate methods for analyzing their structures, as well as for rapid similarity searches in databases. Results: In this article a novel algorithm for an RNA structural comparison SETTER (SEcondary sTructure-based TERtiary Structure Similarity Algorithm) is introduced. SETTER uses a pairwise comparison method based on 3D similarity of the so-called generalized secondary structure units. For each pair of structures, SETTER produces a distance score and an indication of its statistical significance. SETTER can be used both for the structural alignments of structures that are already known to be homologous, as well as for 3D structure similarity searches and functional annotation. The algorithm presented is both accurate and fast and does not impose limits on the size of aligned RNA structures. Motivation: Understanding the architecture and function of RNA molecules requires methods for comparing and analyzing their 3D structures. Although a structural alignment of short RNAs is achievable in a reasonable amount of time, large structures represent much bigger challenge. However, the growth of the number of large RNAs deposited in the PDB database calls for the development of fast and accurate methods for analyzing their structures, as well as for rapid similarity searches in databases. Results: In this article a novel algorithm for an RNA structural comparison SETTER (SEcondary sTructure-based TERtiary Structure Similarity Algorithm) is introduced. SETTER uses a pairwise comparison method based on 3D similarity of the so-called generalized secondary structure units. For each pair of structures, SETTER produces a distance score and an indication of its statistical significance. SETTER can be used both for the structural alignments of structures that are already known to be homologous, as well as for 3D structure similarity searches and functional annotation. The algorithm presented is both accurate and fast and does not impose limits on the size of aligned RNA structures. (en)
Title	Efficient RNA pairwise structure comparison by SETTER method Efficient RNA pairwise structure comparison by SETTER method (en)
skos:prefLabel	Efficient RNA pairwise structure comparison by SETTER method Efficient RNA pairwise structure comparison by SETTER method (en)
skos:notation	RIV/00216208:11320/12:10124054!RIV13-GA0-11320___
http://linked.open...avai/riv/aktivita	P Z
http://linked.open...avai/riv/aktivity	P(GAP202/11/0968), Z(MSM6046137302)
http://linked.open...iv/cisloPeriodika	14
http://linked.open...vai/riv/dodaniDat	2013
http://linked.open...aciTvurceVysledku	Hoksza, David
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Univerzita Karlova v Praze / Matematicko-fyzikální fakulta
http://linked.open...dnocenehoVysledku	133572
http://linked.open...ai/riv/idVysledku	RIV/00216208:11320/12:10124054
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	structural bioinformatics; tertiary structure; secondary structure; RNA (en)
http://linked.open.../riv/klicoveSlovo	RNA structural bioinformatics tertiary structure secondary structure
http://linked.open...odStatuVydavatele	GB - Spojené království Velké Británie a Severního Irska
http://linked.open...ontrolniKodProRIV	[723981CF3518]
http://linked.open...i/riv/nazevZdroje	BIOINFORMATICS
http://linked.open...in/vavai/riv/obor	IN
http://linked.open...ichTvurcuVysledku	1 (xsd:int)
http://linked.open...cetTvurcuVysledku	2 (xsd:int)
http://linked.open...vavai/riv/projekt	Large-scale Nonmetric Similarity Search in Complex Domains
http://linked.open...UplatneniVysledku	2012
http://linked.open...v/svazekPeriodika	28
http://linked.open...iv/tvurceVysledku	Hoksza, David Svozil, Daniel
http://linked.open...ain/vavai/riv/wos	000306136100009
http://linked.open...n/vavai/riv/zamer	Preparation and research of functional materials and material technologies using micro- and nanoscopic methods
issn	1367-4803
number of pages	7 (xsd:int)
http://bibframe.org/vocab/doi	10.1093/bioinformatics/bts301
http://localhost/t...ganizacniJednotka	11320

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