Molecular Dynamics Simulations of Nucleic Acids. From
Tetranucleotides to the Ribosome

J 2014

Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome

ŠPONER, Jiří, Pavel BANÁŠ, Petr JUREČKA, Marie ZGARBOVÁ, Petra KÜHROVÁ et. al.

Základní údaje

Originální název

Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome

Autoři

ŠPONER, Jiří (203 Česká republika, garant, domácí), Pavel BANÁŠ (203 Česká republika), Petr JUREČKA (203 Česká republika), Marie ZGARBOVÁ (203 Česká republika), Petra KÜHROVÁ (203 Česká republika), Marek HAVRILA (703 Slovensko, domácí), Miroslav KREPL (203 Česká republika), Petr STADLBAUER (203 Česká republika) a Michal OTYEPKA (203 Česká republika)

Vydání

The Journal of Physical Chemistry Letters, Washington, American Chemical Society, 2014, 1948-7185

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10403 Physical chemistry

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 7.458

Kód RIV

RIV/00216224:14740/14:00076672

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1021/jz500557y

UT WoS

000336199000027

Klíčová slova anglicky

DELTA-VIRUS RIBOZYME; AMBER FORCE-FIELD; REPLICA-EXCHANGE METHOD; SAM-II RIBOSWITCH; RNA KISSING-LOOP; STRUCTURAL DYNAMICS; QUADRUPLEX DNA; EXPLICIT SOLVENT; ENERGY LANDSCAPES; BINDING-SITES

Štítky

kontrola MP, MP, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 3. 10. 2014 08:55, Olga Křížová

Anotace

V originále

We present a brief overview of explicit solvent molecular dynamics (MD) simulations of nucleic acids. We explain physical chemistry limitations of the simulations, namely, the molecular mechanics (MM) force field (FF) approximation and limited time scale. Further, we discuss relations and differences between simulations and experiments, compare standard and enhanced sampling simulations, discuss the role of starting structures, comment on different versions of nucleic acid FFs, and relate MM computations with contemporary quantum chemistry. Despite its limitations, we show that MD is a powerful technique for studying the structural dynamics of nucleic acids with a fast growing potential that substantially complements experimental results and aids their interpretation.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

Citovat

ŠPONER, Jiří, Pavel BANÁŠ, Petr JUREČKA, Marie ZGARBOVÁ, Petra KÜHROVÁ, Marek HAVRILA, Miroslav KREPL, Petr STADLBAUER a Michal OTYEPKA. Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome. The Journal of Physical Chemistry Letters. Washington: American Chemical Society, 2014, roč. 5, č. 10, s. 1771-1782. ISSN 1948-7185. Dostupné z: https://dx.doi.org/10.1021/jz500557y.

@article{1200003,
   author = {Šponer, Jiří and Banáš, Pavel and Jurečka, Petr and Zgarbová, Marie and Kührová, Petra and Havrila, Marek and Krepl, Miroslav and Stadlbauer, Petr and Otyepka, Michal},
   article_location = {Washington},
   article_number = {10},
   doi = {http://dx.doi.org/10.1021/jz500557y},
   keywords = {DELTA-VIRUS RIBOZYME; AMBER FORCE-FIELD; REPLICA-EXCHANGE METHOD; SAM-II RIBOSWITCH; RNA KISSING-LOOP; STRUCTURAL DYNAMICS; QUADRUPLEX DNA; EXPLICIT SOLVENT; ENERGY LANDSCAPES; BINDING-SITES},
   language = {eng},
   issn = {1948-7185},
   journal = {The Journal of Physical Chemistry Letters},
   title = {Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome},
   url = {http://pubs.acs.org/doi/abs/10.1021/jz500557y},
   volume = {5},
   year = {2014}
}

TY  - JOUR
ID  - 1200003
AU  - Šponer, Jiří - Banáš, Pavel - Jurečka, Petr - Zgarbová, Marie - Kührová, Petra - Havrila, Marek - Krepl, Miroslav - Stadlbauer, Petr - Otyepka, Michal
PY  - 2014
TI  - Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome
JF  - The Journal of Physical Chemistry Letters
VL  - 5
IS  - 10
SP  - 1771-1782
EP  - 1771-1782
PB  - American Chemical Society
SN  - 19487185
KW  - DELTA-VIRUS RIBOZYME
KW  - AMBER FORCE-FIELD
KW  - REPLICA-EXCHANGE METHOD
KW  - SAM-II RIBOSWITCH
KW  - RNA KISSING-LOOP
KW  - STRUCTURAL DYNAMICS
KW  - QUADRUPLEX DNA
KW  - EXPLICIT SOLVENT
KW  - ENERGY LANDSCAPES
KW  - BINDING-SITES
UR  - http://pubs.acs.org/doi/abs/10.1021/jz500557y
L2  - http://pubs.acs.org/doi/abs/10.1021/jz500557y
N2  - We present a brief overview of explicit solvent molecular dynamics (MD) simulations of nucleic acids. We explain physical chemistry limitations of the simulations, namely, the molecular mechanics (MM) force field (FF) approximation and limited time scale. Further, we discuss relations and differences between simulations and experiments, compare standard and enhanced sampling simulations, discuss the role of starting structures, comment on different versions of nucleic acid FFs, and relate MM computations with contemporary quantum chemistry. Despite its limitations, we show that MD is a powerful technique for studying the structural dynamics of nucleic acids with a fast growing potential that substantially complements experimental results and aids their interpretation.
ER  -

ŠPONER, Jiří, Pavel BANÁŠ, Petr JUREČKA, Marie ZGARBOVÁ, Petra KÜHROVÁ, Marek HAVRILA, Miroslav KREPL, Petr STADLBAUER a Michal OTYEPKA. Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome. \textit{The Journal of Physical Chemistry Letters}. Washington: American Chemical Society, 2014, roč.~5, č.~10, s.~1771-1782. ISSN~1948-7185. Dostupné z: https://dx.doi.org/10.1021/jz500557y.

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