Structural Insights into the Osteopontin-Aptamer Complex by Molecular Dynamics Simulations

Frontiers in Chemistry ◽

10.3389/fchem.2018.00002 ◽

2018 ◽

Vol 6 ◽

Author(s):

Giovanni La Penna ◽

Riccardo Chelli

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Dynamics Simulations ◽

Structural Insights

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Structural Insights into the Two Sequential Folding Transition States of the PB1 Domain of NBR1 from Φ Value Analysis and Biased Molecular Dynamics Simulations

Biochemistry ◽

10.1021/bi1016793 ◽

2011 ◽

Vol 50 (1) ◽

pp. 125-135 ◽

Author(s):

Ping Chen ◽

Clare-Louise Evans ◽

Jonathan D. Hirst ◽

Mark S. Searle

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Transition States ◽

Value Analysis ◽

Dynamics Simulations ◽

Structural Insights

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Molecular dynamics simulations reveal structural insights into inhibitor binding modes and functionality in human Group IIA phospholipase A2

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.25235 ◽

2017 ◽

Vol 85 (5) ◽

pp. 827-842 ◽

Author(s):

Ryung Rae Kim ◽

Alpeshkumar K. Malde ◽

Alireza Nematollahi ◽

Kieran F. Scott ◽

W. Bret Church

Keyword(s):

Molecular Dynamics ◽

Phospholipase A2 ◽

Molecular Dynamics Simulations ◽

Binding Modes ◽

Human Group ◽

Inhibitor Binding ◽

Dynamics Simulations ◽

Structural Insights ◽

Group Iia Phospholipase A2

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Structural insights by molecular dynamics simulations into specificity of the major human AP endonuclease toward the benzene-derived DNA adduct, pBQ-C

Nucleic Acids Research ◽

10.1093/nar/gkh594 ◽

2004 ◽

Vol 32 (9) ◽

pp. 2844-2852 ◽

Author(s):

A. B. Guliaev

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Ap Endonuclease ◽

Dynamics Simulations ◽

Structural Insights

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Structural insights into the binding mode of d-sorbitol with sorbitol dehydrogenase using QM-polarized ligand docking and molecular dynamics simulations

Biochemical Engineering Journal ◽

10.1016/j.bej.2016.07.008 ◽

2016 ◽

Vol 114 ◽

pp. 244-256 ◽

Author(s):

Chandrabose Selvaraj ◽

Gopinath Krishnasamy ◽

Sujit Sadashiv Jagtap ◽

Sanjay K.S. Patel ◽

Saurabh Sudha Dhiman ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Binding Mode ◽

Sorbitol Dehydrogenase ◽

Ligand Docking ◽

Dynamics Simulations ◽

Structural Insights

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Structural insights by molecular dynamics simulations into differential repair efficiency for ethano-A versus etheno-A adducts by the human alkylpurine-DNA N-glycosylase

Nucleic Acids Research ◽

10.1093/nar/gkf494 ◽

2002 ◽

Vol 30 (17) ◽

pp. 3778-3787 ◽

Author(s):

A. B. Guliaev

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Repair Efficiency ◽

Dynamics Simulations ◽

Structural Insights

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Multipolar/Polarizable Molecular Dynamics Simulations of Liquid-Liquid Extraction of Benzene from Hydrocarbons Using Ionic Liquids

10.26434/chemrxiv.8239829.v1 ◽

2019 ◽

Author(s):

Erik A. Vazquez-Montelongo ◽

G. Andres Cisneros ◽

Hugo Flores

Keyword(s):

Molecular Dynamics ◽

Ionic Liquids ◽

Molecular Dynamics Simulations ◽

Liquid Extraction ◽

Liquid Liquid Extraction ◽

Dynamics Simulations ◽

Structural Insights

<div><p>We used AMOEBA to explore the capacity of 1,3 dimethylimidazolium tetrafluorobrorate, [DMIM][BF4], </p> <p>and ethyl-methylimidazolium tetrafluorobrorate, [EMIM][BF4], to extract benzene from a mixture of benzene-dodecane. Our results indicate that [DMIM][BF4] exhibits better selectivity and provide structural insights on possible reasons for the observed preference.</p><br></div>

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Functional and Structural Insights Revealed by Molecular Dynamics Simulations of an Essential RNA Editing Ligase in Trypanosoma

SciVee ◽

10.4016/5585.01 ◽

2007 ◽

Author(s):

Rommie Amaro ◽

Robert Swift ◽

J. McCammon

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Rna Editing ◽

Dynamics Simulations ◽

Structural Insights

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Molecular dynamics simulations reveal structural insights into inhibitor binding modes and mechanism of casein kinase II inhibitors

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2018.1450166 ◽

2018 ◽

Vol 37 (5) ◽

pp. 1120-1135 ◽

Author(s):

Zaheer Ul-Haq ◽

Sajda Ashraf ◽

Majdi M. Bkhaitan

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Casein Kinase Ii ◽

Casein Kinase ◽

Binding Modes ◽

Inhibitor Binding ◽

Dynamics Simulations ◽

Structural Insights

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Structural insights into the effect of isonucleosides on B-DNA duplexes using molecular-dynamics simulations

Journal of Molecular Modeling ◽

10.1007/s00894-005-0085-8 ◽

2006 ◽

Vol 12 (6) ◽

pp. 781-791 ◽

Author(s):

Hongwei Jin ◽

Suxin Zheng ◽

Zhanli Wang ◽

Cheng Luo ◽

Jianhua Shen ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Dna Duplexes ◽

Dynamics Simulations ◽

Structural Insights

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Molecular Dynamics Simulations of the Circadian Clock Protein Kaic Reveal Structural Insights into the Nucleotide Release and Circadian Timing Mechanisms

Biophysical Journal ◽

10.1016/j.bpj.2018.11.1680 ◽

2019 ◽

Vol 116 (3) ◽

pp. 310a

Author(s):

Lu Hong ◽

Bodhi P. Vani ◽

Erik H. Thiede ◽

Michael J. Rust ◽

Aaron R. Dinner

Keyword(s):

Molecular Dynamics ◽

Circadian Clock ◽

Molecular Dynamics Simulations ◽

Circadian Timing ◽

Timing Mechanisms ◽

Nucleotide Release ◽

Dynamics Simulations ◽

Structural Insights ◽

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