SETTER - RNA SEcondary sTructure-based TERtiary Structure Similarity Algorithm

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60461373%3A22310%2F11%3A43892044" target="_blank" >RIV/60461373:22310/11:43892044 - isvavai.cz</a>

Výsledek na webu

<a href="http://dx.doi.org/10.1007/978-3-642-21260-4_8" target="_blank" >http://dx.doi.org/10.1007/978-3-642-21260-4_8</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1007/978-3-642-21260-4_8" target="_blank" >10.1007/978-3-642-21260-4_8</a>

Jazyk výsledku

angličtina

Název v původním jazyce

SETTER - RNA SEcondary sTructure-based TERtiary Structure Similarity Algorithm

Popis výsledku v původním jazyce

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 textbf{SETTER} (RNA textbf{SE}condary stextbf{T}ructure-based textbf{TER}tiary structure similarity) based on partitioning of RNA structures into so-called generalized secondary structure units (GSSU). We introduce a fast similarity method exploiting RMSD-basedalgorithm 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 alsoa 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.

Název v anglickém jazyce

SETTER - RNA SEcondary sTructure-based TERtiary Structure Similarity Algorithm

Popis výsledku anglicky

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 textbf{SETTER} (RNA textbf{SE}condary stextbf{T}ructure-based textbf{TER}tiary structure similarity) based on partitioning of RNA structures into so-called generalized secondary structure units (GSSU). We introduce a fast similarity method exploiting RMSD-basedalgorithm 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 alsoa 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.

Druh

D - Stať ve sborníku

CEP obor

IN - Informatika

OECD FORD obor

—

Projekt

—

Návaznosti

Z - Vyzkumny zamer (s odkazem do CEZ)

Rok uplatnění

2011

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název statě ve sborníku

ISBRA'11 Proceedings of the 7th international conference on Bioinformatics research and applications

ISBN

978-3-642-21259-8

ISSN

0302-9743

e-ISSN

—

Počet stran výsledku

12

Strana od-do

37-48

Název nakladatele

SPRINGER

Místo vydání

Berlin

Místo konání akce

Changsha, China

Datum konání akce

27. 5. 2011

Typ akce podle státní příslušnosti

WRD - Celosvětová akce

Kód UT WoS článku

000296688700008