Molecular Dynamics Simulations of 441 Two-Residue Peptides in Aqueous Solution: Conformational Preferences and Neighboring Residue Effects with the Amber ff99SB-ildn-NMR Force Field

Shuxiang Li; Casey T. Andrews; Tamara Frembgen-Kesner; Mark S. Miller; Stephen L. Siemonsma; Timothy D. Collingsworth; Isaac T. Rockafellow; Nguyet Anh Ngo; Brady A. Campbell; Reid F. Brown; Chengxuan Guo; Michael Schrodt; Yu-Tsan Liu; Adrian H. Elcock

doi:10.1021/ct5010966

Molecular Dynamics Simulations of 441 Two-Residue Peptides in Aqueous Solution: Conformational Preferences and Neighboring Residue Effects with the Amber ff99SB-ildn-NMR Force Field

Journal of Chemical Theory and Computation ◽

10.1021/ct5010966 ◽

2015 ◽

Vol 11 (3) ◽

pp. 1315-1329 ◽

Cited By ~ 9

Author(s):

Shuxiang Li ◽

Casey T. Andrews ◽

Tamara Frembgen-Kesner ◽

Mark S. Miller ◽

Stephen L. Siemonsma ◽

...

Keyword(s):

Molecular Dynamics ◽

Aqueous Solution ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Conformational Preferences ◽

Dynamics Simulations ◽

Neighboring Residue

Ab initio force field for simulations of proteins and nucleic acids: Application to molecular dynamics simulations in aqueous solution

Computer Aided Innovation of New Materials II ◽

10.1016/b978-0-444-89778-7.50070-0 ◽

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Author(s):

M. Aida ◽

G. Corongiu ◽

E. Clementi

Keyword(s):

Molecular Dynamics ◽

Aqueous Solution ◽

Nucleic Acids ◽

Force Field ◽

Ab Initio ◽

Molecular Dynamics Simulations ◽

Dynamics Simulations

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pp. 1902-1915 ◽

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Oleg Borodin ◽

Dmitry Bedrov ◽

Grant D. Smith

Keyword(s):

Molecular Dynamics ◽

Aqueous Solution ◽

Ethylene Oxide ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Polarizable Force Field ◽

Poly Ethylene Oxide ◽

Poly Ethylene ◽

Dynamics Simulations

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10.1039/c4ra09897h ◽

2014 ◽

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Sam Mulholland ◽

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Boyan B. Bonev ◽

Jonathan D. Hirst

Keyword(s):

Molecular Dynamics ◽

Amino Acid ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Amino Acid Residues ◽

Charmm Force Field ◽

Force Field Parameters ◽

Dynamics Simulations

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Journal of Biomolecular Structure and Dynamics ◽

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2014 ◽

Vol 33 (4) ◽

pp. 789-803 ◽

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Joel B. Alderete ◽

Karen R. Navarrete

Keyword(s):

Molecular Dynamics ◽

Antitumor Activity ◽

Molecular Dynamics Simulations ◽

Binding Modes ◽

Conformational Preferences ◽

Tubulin Binding ◽

Structural Insight ◽

Dynamics Simulations ◽

Insight Into

Trimethylamine-N-oxide: its hydration structure, surface activity, and biological function, viewed by vibrational spectroscopy and molecular dynamics simulations

Physical Chemistry Chemical Physics ◽

10.1039/c6cp07284d ◽

2017 ◽

Vol 19 (10) ◽

pp. 6909-6920 ◽

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Johannes Hunger ◽

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Wataru Mizukami ◽

Mischa Bonn ◽

...

Keyword(s):

Molecular Dynamics ◽

Aqueous Solution ◽

Molecular Dynamics Simulations ◽

Surface Activity ◽

Vibrational Spectroscopy ◽

Biological Function ◽

Molecular Simulations ◽

Structure Surface ◽

Dynamics Simulations ◽

Hydrophilicity And Hydrophobicity

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Frequency-dependent local field factors in dielectric liquids by a polarizable force field and molecular dynamics simulations

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Nazanin Davari ◽

Shokouh Haghdani ◽

Per-Olof Åstrand

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Local Field ◽

Frequency Dependent ◽

Polarizable Force Field ◽

Dielectric Liquids ◽

Dynamics Simulations

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The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.8b07736 ◽

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Keyword(s):

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Force Field ◽

Molecular Dynamics Simulations ◽

Theoretical Study ◽

Field Development ◽

Force Field Development ◽

Dynamics Simulations

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Fritz K. Winkler ◽

Wilfred F. van Gunsteren ◽

...

Keyword(s):

Molecular Dynamics ◽

Aqueous Solution ◽

Molecular Dynamics Simulations ◽

Peptide Derivatives ◽

C And N ◽

Dynamics Simulations ◽

Derivatives Of

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Aqueous Solution ◽

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Boron Nitride Nanotubes ◽

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