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@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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