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Template-based prediction of RNA tertiary structure

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    0472689 - MBÚ 2017 RIV US eng C - Conference Paper (international conference)
    Galvánek, R. - Hoksza, D. - Pánek, Josef
    Template-based prediction of RNA tertiary structure.
    2016 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE (BIBM). Los Alamitos: EEE COMPUTER SOC, 2016 - (Tian,, T.; Jiang, Q.; Liu, Y.; Burrage, K.; Song, J.; Wang, Y.; Hu, X.; Morishita, S.; Zhu, Q.; Wang, G.), s. 1897-1900. EEE International Conference on Bioinformatics and Biomedicine-BIBM. ISBN 978-1-5090-1610-5. ISSN 2156-1125.
    [IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM). Shenzhen (CN), 15.12.2016-18.12.2016]
    R&D Projects: GA ČR GA15-00885S
    Institutional support: RVO:61388971
    Keywords : RNA tertiary structure * prediction of RNA * size of hundreds of nucleotides
    Subject RIV: EE - Microbiology, Virology

    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.
    Permanent Link: http://hdl.handle.net/11104/0269927

     
     
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