Tytuł
RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures
Autorzy
[ 1 ] Instytut Chemii Bioorganicznej Polskiej Akademii Nauk, Polska Akademia Nauk | [ P ] pracownik
Dyscyplina naukowa (Ustawa 2.0)
[2.3] Informatyka techniczna i telekomunikacja[7.6] Nauki chemiczne
Rok publikacji
2018
Opublikowano w
Typ artykułu
artykuł naukowy
Język publikacji
angielski
Słowa kluczowe
Streszczenie
EN Background: Computational RNA 3D structure prediction and modeling are rising as complementary approaches to high-resolution experimental techniques for structure determination. They often apply to substitute or complement them. Recently, researchers' interests have directed towards in silico methods to fit, remodel and refine RNA tertiary structure models. Their power lies in a problem-specific exploration of RNA conformational space and efficient optimization procedures. The aim is to improve the accuracy of models obtained either computationally or experimentally. Results: Here, we present RNAfitme, a versatile webserver tool for remodeling of nucleobase- and nucleoside residue conformations in the fixed-backbone RNA 3D structures. Our approach makes use of dedicated libraries that define RNA conformational space. They have been built upon torsional angle characteristics of PDB deposited RNA structures. RNAfitme can be applied to reconstruct full-atom model of RNA from its backbone; remodel user-selected nucleobase/nucleoside residues in a given RNA structure; predict RNA 3D structure based on the sequence and the template of a homologous molecule of the same size; refine RNA 3D model by reducing steric clashes indicated during structure quality assessment RNAfitme is a publicly available tool with an intuitive interface. It is freely accessible at http://rnafitme.cs.put.poznan.pl/ Conclusions: RNAfitme has been applied in various RNA 3D remodeling scenarios for several types of input data. Computational experiments proved its efficiency, accuracy, and usefulness in the processing of RNAs of any size. Fidelity of RNAfitme predictions has been thoroughly tested for RNA 3D structures determined experimentally and modeled in silico.
Strony (od-do)
304
Typ licencji
CC BY (uznanie autorstwa)
Wersja tekstu w otwartym dostępie
ostateczna wersja opublikowana
Data udostępnienia
08.2018
Czas udostępnienia publikacji w sposób otwarty
w momencie opublikowania
Punktacja Ministerstwa / czasopismo
35
Punktacja Ministerstwa / czasopismo w ewaluacji 2017-2021
35
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