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RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

The result's identifiers

  • Result code in IS VaVaI

    <a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F18%3A00492310" target="_blank" >RIV/68081707:_____/18:00492310 - isvavai.cz</a>

  • Alternative codes found

    RIV/61989592:15310/18:73591542

  • Result on the web

    <a href="https://pubs.acs.org/doi/10.1021/acs.chemrev.7b00427" target="_blank" >https://pubs.acs.org/doi/10.1021/acs.chemrev.7b00427</a>

  • DOI - Digital Object Identifier

    <a href="http://dx.doi.org/10.1021/acs.chemrev.7b00427" target="_blank" >10.1021/acs.chemrev.7b00427</a>

Alternative languages

  • Result language

    angličtina

  • Original language name

    RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

  • Original language description

    With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.

  • Czech name

  • Czech description

Classification

  • Type

    J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database

  • CEP classification

  • OECD FORD branch

    10608 - Biochemistry and molecular biology

Result continuities

  • Project

    Result was created during the realization of more than one project. More information in the Projects tab.

  • Continuities

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

Others

  • Publication year

    2018

  • Confidentiality

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

Data specific for result type

  • Name of the periodical

    Chemical Reviews

  • ISSN

    0009-2665

  • e-ISSN

    1520-6890

  • Volume of the periodical

    118

  • Issue of the periodical within the volume

    8

  • Country of publishing house

    US - UNITED STATES

  • Number of pages

    162

  • Pages from-to

    4177-4338

  • UT code for WoS article

    000431095200004

  • EID of the result in the Scopus database

    2-s2.0-85045378342