Template-based prediction of RNA tertiary structure

Result code in 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>

Alternative codes found

RIV/00216208:11320/16:10328149

Result on the web

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DOI - Digital Object Identifier

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Result language

angličtina

Original language name

Template-based prediction of RNA tertiary structure

Original language description

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.

Czech name

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Czech description

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Type

D - Article in proceedings

CEP classification

EE - Microbiology, virology

OECD FORD branch

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Project

<a href="/en/project/GA15-00885S" target="_blank" >GA15-00885S: Novel methods for computational prediction and visualization of secondary structures of ribosomal ribonucleic acids - an integrated solution</a><br>

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2016

Confidentiality

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

Article name in the collection

2016 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE (BIBM)

ISBN

978-1-5090-1610-5

ISSN

2156-1125

e-ISSN

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Number of pages

4

Pages from-to

1897-1900

Publisher name

EEE COMPUTER SOC

Place of publication

Los Alamitos

Event location

Shenzhen

Event date

Dec 15, 2016

Type of event by nationality

WRD - Celosvětová akce

UT code for WoS article

000393191700323