About: SETTER - RNA SEcondary sTructure-based TERtiary Structure Similarity Algorithm

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
rdfs:seeAlso	http://www.springerlink.com/content/m58w38710uh34771/
Description	The recent interest in function of various RNA structures, reflected in the growth of solved RNA structures in PDB, calls for methods for effective and efficient similarity search in RNA structural databases. Here, we propose a method called SETTER (RNA SEcondary sTructure-based TERtiary structure similarity) based on partitioning of RNA structures into so-called generalized secondary structure units (CSSU). We introduce a. fast similarity method exploiting RMSD-based algorithm allowing to assess distance to a pair of GSSU, and a method for aggregating these partial distances into a final distance corresponding to structural similarity of the examined RNA structures. Our algorithm yields not only the distance but also a superposition allowing to visualize the structural similarity. Comparative experiments show that our proposed method is competitive with the best; existing solutions, both in terms of effectiveness and efficiency. The recent interest in function of various RNA structures, reflected in the growth of solved RNA structures in PDB, calls for methods for effective and efficient similarity search in RNA structural databases. Here, we propose a method called SETTER (RNA SEcondary sTructure-based TERtiary structure similarity) based on partitioning of RNA structures into so-called generalized secondary structure units (CSSU). We introduce a. fast similarity method exploiting RMSD-based algorithm allowing to assess distance to a pair of GSSU, and a method for aggregating these partial distances into a final distance corresponding to structural similarity of the examined RNA structures. Our algorithm yields not only the distance but also a superposition allowing to visualize the structural similarity. Comparative experiments show that our proposed method is competitive with the best; existing solutions, both in terms of effectiveness and efficiency. (en)
Title	SETTER - RNA SEcondary sTructure-based TERtiary Structure Similarity Algorithm SETTER - RNA SEcondary sTructure-based TERtiary Structure Similarity Algorithm (en)
skos:prefLabel	SETTER - RNA SEcondary sTructure-based TERtiary Structure Similarity Algorithm SETTER - RNA SEcondary sTructure-based TERtiary Structure Similarity Algorithm (en)
skos:notation	RIV/00216208:11320/11:10099578!RIV13-GA0-11320___
http://linked.open...avai/predkladatel	Matematicko-fyzikální fakulta
http://linked.open...avai/riv/aktivita	P
http://linked.open...avai/riv/aktivity	P(GA201/09/0683)
http://linked.open...iv/cisloPeriodika	5
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	229026
http://linked.open...ai/riv/idVysledku	RIV/00216208:11320/11:10099578
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	structural bioinformatics; similarity search; bioinformatics; RNA (en)
http://linked.open.../riv/klicoveSlovo	similarity search RNA bioinformatics structural bioinformatics
http://linked.open...odStatuVydavatele	DE - Spolková republika Německo
http://linked.open...ontrolniKodProRIV	[D096CAD699A3]
http://linked.open...i/riv/nazevZdroje	Lecture Notes in 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	Similarity searching in very large multimedia databases
http://linked.open...UplatneniVysledku	2011
http://linked.open...v/svazekPeriodika	6674
http://linked.open...iv/tvurceVysledku	Hoksza, David Svozil, Daniel
http://linked.open...ain/vavai/riv/wos	000296688700008
issn	0302-9743
number of pages	12 (xsd:int)
http://localhost/t...ganizacniJednotka	11320
is http://linked.open...avai/riv/vysledek of	SETTER - RNA SEcondary sTructure-based TERtiary Structure Similarity Algorithm

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