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231225s2020 xx |||||o 00| ||eng c |
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|a 10.1002/jcc.26067
|2 doi
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|a pubmed24n1354.xml
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|a (DE-627)NLM301265267
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|a (NLM)31518010
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|a DE-627
|b ger
|c DE-627
|e rakwb
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| 041 |
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|a eng
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| 100 |
1 |
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|a Lin, Fang-Yu
|e verfasserin
|4 aut
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| 245 |
1 |
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|a Improved Modeling of Cation-π and Anion-Ring Interactions Using the Drude Polarizable Empirical Force Field for Proteins
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|c 2020
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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
|b cr
|2 rdacarrier
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|a Date Completed 29.06.2021
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|a Date Revised 29.03.2024
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|a published: Print-Electronic
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|a Citation Status MEDLINE
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| 520 |
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|a © 2019 Wiley Periodicals, Inc.
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|a Cation-π interactions are noncovalent interactions between a π-electron system and a positively charged ion that are regarded as a strong noncovalent interaction and are ubiquitous in biological systems. Similarly, though less studied, anion-ring interactions are present in proteins along with in-plane interactions of anions with aromatic rings. As these interactions are between a polarizing ion and a polarizable π system, the accuracy of the treatment of these interactions in molecular dynamics (MD) simulations using additive force fields (FFs) may be limited. In the present work, to allow for a better description of ion-π interactions in proteins in the Drude-2013 protein polarizable FF, we systematically optimized the parameters for these interactions targeting model compound quantum mechanical (QM) interaction energies with atom pair-specific Lennard-Jones parameters along with virtual particles as selected ring centroids introduced to target the QM interaction energies and geometries. Subsequently, MD simulations were performed on a series of protein structures where ion-π pairs occur to evaluate the optimized parameters in the context of the Drude-2013 FF. The resulting FF leads to a significant improvement in reproducing the ion-π pair distances observed in experimental protein structures, as well as a smaller root-mean-square differences and fluctuations of the overall protein structures from experimental structures. Accordingly, the optimized Drude-2013 protein polarizable FF is suggested for use in MD simulations of proteins where cation-π and anion-ring interactions are critical. © 2019 Wiley Periodicals, Inc
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|a Journal Article
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| 650 |
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|a Research Support, N.I.H., Extramural
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| 650 |
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4 |
|a Research Support, Non-U.S. Gov't
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| 650 |
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4 |
|a CHARMM
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| 650 |
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4 |
|a molecular dynamics
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| 650 |
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4 |
|a noncovalent interactions
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| 650 |
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4 |
|a polarizable force field
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| 650 |
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4 |
|a quantum mechanics
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| 650 |
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7 |
|a Anions
|2 NLM
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| 650 |
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7 |
|a Cations
|2 NLM
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| 650 |
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7 |
|a Proteins
|2 NLM
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| 700 |
1 |
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|a MacKerell, Alexander D
|c Jr
|e verfasserin
|4 aut
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| 773 |
0 |
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|i Enthalten in
|t Journal of computational chemistry
|d 1984
|g 41(2020), 5 vom: 15. Feb., Seite 439-448
|w (DE-627)NLM098138448
|x 1096-987X
|7 nnns
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| 773 |
1 |
8 |
|g volume:41
|g year:2020
|g number:5
|g day:15
|g month:02
|g pages:439-448
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| 856 |
4 |
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|u http://dx.doi.org/10.1002/jcc.26067
|3 Volltext
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|a AR
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|d 41
|j 2020
|e 5
|b 15
|c 02
|h 439-448
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