Template-based prediction of RNA tertiary structure

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388971%3A_____%2F16%3A00472689" target="_blank" >RIV/61388971:_____/16:00472689 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/00216208:11320/16:10328149

Výsledek na webu

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DOI - Digital Object Identifier

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Jazyk výsledku

angličtina

Název v původním jazyce

Template-based prediction of RNA tertiary structure

Popis výsledku v původním jazyce

RNA tertiary structure prediction approaches can be divided into two groups: de novo methods and template-based modeling. De novo are applicable only for small molecules while in case of medium and large size RNA molecules, template-based modeling needs to be employed. While this type of modeling is quite common in protein structure prediction field, there exist only very few tools for template-based RNA structure prediction. Therefore, we present a methodology for prediction of RNA three dimensional structure (target) utilizing a known structure of a related RNA molecule (template). First, the target and template sequences are aligned. Next, sequentially similar regions in the alignment are identified and corresponding substructures are transferred from template to target. The remaining parts of the target structures are predicted using an external tool. This phase includes treatment of indels and valid linking of the transferred and predicted portions of the target structure. Our proposed method is able to predict even large ribosomal RNA structures when sufficiently similar template is available. The experiments have shown that the main impact on the quality of prediction has the sequence similarity of the template and target and number of indels. For structures with size of hundreds of nucleotides with sequence similarity with template over 50% and ratio of indels up to 50% the method is able to generate target structures up to ten RMSD with respect to the reference structure.

Název v anglickém jazyce

Template-based prediction of RNA tertiary structure

Popis výsledku anglicky

RNA tertiary structure prediction approaches can be divided into two groups: de novo methods and template-based modeling. De novo are applicable only for small molecules while in case of medium and large size RNA molecules, template-based modeling needs to be employed. While this type of modeling is quite common in protein structure prediction field, there exist only very few tools for template-based RNA structure prediction. Therefore, we present a methodology for prediction of RNA three dimensional structure (target) utilizing a known structure of a related RNA molecule (template). First, the target and template sequences are aligned. Next, sequentially similar regions in the alignment are identified and corresponding substructures are transferred from template to target. The remaining parts of the target structures are predicted using an external tool. This phase includes treatment of indels and valid linking of the transferred and predicted portions of the target structure. Our proposed method is able to predict even large ribosomal RNA structures when sufficiently similar template is available. The experiments have shown that the main impact on the quality of prediction has the sequence similarity of the template and target and number of indels. For structures with size of hundreds of nucleotides with sequence similarity with template over 50% and ratio of indels up to 50% the method is able to generate target structures up to ten RMSD with respect to the reference structure.

Druh

D - Stať ve sborníku

CEP obor

EE - Mikrobiologie, virologie

OECD FORD obor

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Projekt

<a href="/cs/project/GA15-00885S" target="_blank" >GA15-00885S: Nové metody pro předpověď a vizualizaci sekundárních struktur ribozomálních ribonukleových kyselin - integrované řešení</a><br>

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2016

Kód důvěrnosti údajů

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

Název statě ve sborníku

2016 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE (BIBM)

ISBN

978-1-5090-1610-5

ISSN

2156-1125

e-ISSN

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Počet stran výsledku

4

Strana od-do

1897-1900

Název nakladatele

EEE COMPUTER SOC

Místo vydání

Los Alamitos

Místo konání akce

Shenzhen

Datum konání akce

15. 12. 2016

Typ akce podle státní příslušnosti

WRD - Celosvětová akce

Kód UT WoS článku

000393191700323