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%2F00216208%3A11320%2F11%3A10099578" target="_blank" >RIV/00216208:11320/11:10099578 - isvavai.cz</a>

Výsledek na webu

<a href="http://www.springerlink.com/content/m58w38710uh34771/" target="_blank" >http://www.springerlink.com/content/m58w38710uh34771/</a>

DOI - Digital Object Identifier

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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 SETTER (RNASEcondary 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.

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 SETTER (RNASEcondary 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.

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

IN - Informatika

OECD FORD obor

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Projekt

<a href="/cs/project/GA201%2F09%2F0683" target="_blank" >GA201/09/0683: Vyhledávání v rozsáhlých multimediálních databázích</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2011

Kód důvěrnosti údajů

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

Název periodika

Lecture Notes in Bioinformatics

ISSN

0302-9743

e-ISSN

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Svazek periodika

6674

Číslo periodika v rámci svazku

5

Stát vydavatele periodika

DE - Spolková republika Německo

Počet stran výsledku

12

Strana od-do

37-48

Kód UT WoS článku

000296688700008

EID výsledku v databázi Scopus

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