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231224s2016 xx |||||o 00| ||eng c |
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|a 10.1002/jcc.24307
|2 doi
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|a pubmed24n0857.xml
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|a DE-627
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|e rakwb
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|a eng
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| 100 |
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|a Xu, You
|e verfasserin
|4 aut
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|a Additive CHARMM force field for naturally occurring modified ribonucleotides
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|c 2016
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|a Text
|b txt
|2 rdacontent
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|a ƒaComputermedien
|b c
|2 rdamedia
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|a ƒa Online-Ressource
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|a Date Completed 10.11.2016
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|a Date Revised 09.09.2021
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|a published: Print-Electronic
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|a Citation Status MEDLINE
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|a © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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|a More than 100 naturally occurring modified nucleotides have been found in RNA molecules, in particular in tRNAs. We have determined molecular mechanics force field parameters compatible with the CHARMM36 all-atom additive force field for all these modifications using the CHARMM force field parametrization strategy. Emphasis was placed on fine tuning of the partial atomic charges and torsion angle parameters. Quantum mechanics calculations on model compounds provided the initial set of target data, and extensive molecular dynamics simulations of nucleotides and oligonucleotides in aqueous solutions were used for further refinement against experimental data. The presented parameters will allow for computational studies of a wide range of RNAs containing modified nucleotides, including the ribosome and transfer RNAs
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|a Journal Article
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|a Research Support, N.I.H., Extramural
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|a Research Support, Non-U.S. Gov't
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|a RNA
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|a empirical force field
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|a molecular dynamics
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|a nucleic acids
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|a oligonucleotide
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|a transfer RNA
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|a Ribonucleotides
|2 NLM
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|a RNA
|2 NLM
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|a 63231-63-0
|2 NLM
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1 |
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|a Vanommeslaeghe, Kenno
|e verfasserin
|4 aut
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1 |
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|a Aleksandrov, Alexey
|e verfasserin
|4 aut
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| 700 |
1 |
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|a MacKerell, Alexander D
|c Jr
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Nilsson, Lennart
|e verfasserin
|4 aut
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| 773 |
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|i Enthalten in
|t Journal of computational chemistry
|d 1984
|g 37(2016), 10 vom: 15. Apr., Seite 896-912
|w (DE-627)NLM098138448
|x 1096-987X
|7 nnns
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| 773 |
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|g volume:37
|g year:2016
|g number:10
|g day:15
|g month:04
|g pages:896-912
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|u http://dx.doi.org/10.1002/jcc.24307
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