Solution structure of a conserved DNA sequence from the HIV-1 genome: Restrained molecular dynamics simulation with distance and torsion angle restraints derived from two-dimensional NMR spectra

Anwer Mujeeb; Sean M. Kerwin; George L. Kenyon; Thomas L. James

doi:10.1021/bi00212a007

Solution structure of a conserved DNA sequence from the HIV-1 genome: Restrained molecular dynamics simulation with distance and torsion angle restraints derived from two-dimensional NMR spectra

Biochemistry ◽

10.1021/bi00212a007 ◽

1993 ◽

Vol 32 (49) ◽

pp. 13419-13431 ◽

Cited By ~ 47

Author(s):

Anwer Mujeeb ◽

Sean M. Kerwin ◽

George L. Kenyon ◽

Thomas L. James

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dna Sequence ◽

Torsion Angle ◽

Nmr Spectra ◽

Solution Structure ◽

Dynamics Simulation ◽

Two Dimensional ◽

Hiv 1 ◽

Restrained Molecular Dynamics

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Solution structure of a DNA octamer containing the pribnow box via restrained molecular dynamics simulation with distance and torsion angle constraints derived from two-dimensional nuclear magnetic resonance spectral fitting

Journal of Molecular Biology ◽

10.1016/0022-2836(92)90904-x ◽

1992 ◽

Vol 227 (2) ◽

pp. 510-531 ◽

Cited By ~ 44

Author(s):

Uli Schmitz ◽

Ingmar Sethson ◽

William M. Egan ◽

Thomas L. James

Keyword(s):

Molecular Dynamics ◽

Nuclear Magnetic Resonance ◽

Molecular Dynamics Simulation ◽

Magnetic Resonance ◽

Torsion Angle ◽

Solution Structure ◽

Dynamics Simulation ◽

Two Dimensional ◽

Spectral Fitting ◽

Pribnow Box

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Solution Structure Studies of the Cobalt Complex of a Bleomycin Functional Model Bound to d(CGCAATTGCG)2by Two-Dimensional Nuclear Magnetic Resonance Methods and Restrained Molecular Dynamics Simulation

Bioconjugate Chemistry ◽

10.1021/bc960065k ◽

1996 ◽

Vol 7 (6) ◽

pp. 670-679 ◽

Cited By ~ 3

Author(s):

Yanwu Yang ◽

Liren Huang ◽

Richard T. Pon ◽

Shu-Fang Cheng ◽

Ding-Kwo Chang ◽

...

Keyword(s):

Molecular Dynamics ◽

Nuclear Magnetic Resonance ◽

Molecular Dynamics Simulation ◽

Magnetic Resonance ◽

Solution Structure ◽

Cobalt Complex ◽

Functional Model ◽

Dynamics Simulation ◽

Two Dimensional ◽

Restrained Molecular Dynamics

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Solution Structure of HIV-1 Protease Flaps Probed by Comparison of Molecular Dynamics Simulation Ensembles and EPR Experiments

Journal of the American Chemical Society ◽

10.1021/ja800893d ◽

2008 ◽

Vol 130 (23) ◽

pp. 7184-7185 ◽

Cited By ~ 48

Author(s):

Fangyu Ding ◽

Melinda Layten ◽

Carlos Simmerling

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Solution Structure ◽

Dynamics Simulation ◽

Epr Experiments ◽

Hiv 1

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Solution Structure of HIV-1 Protease-Allophenylnorstatine Derivative Inhibitor Complex Obtained from Molecular Dynamics Simulation.

Chemical and Pharmaceutical Bulletin ◽

10.1248/cpb.42.176 ◽

1994 ◽

Vol 42 (1) ◽

pp. 176-178 ◽

Cited By ~ 12

Author(s):

Ryohei KATO ◽

Osamu TAKAHASHI ◽

Yoshiaki KISO ◽

Ikuo MORIGUCHI ◽

Shuichi HIRONO

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Solution Structure ◽

Dynamics Simulation ◽

Inhibitor Complex ◽

Hiv 1

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Molecular Docking and Molecular Dynamics Simulation Based Approach to Explore the Dual Inhibitor Against HIV-1 Reverse Transcriptase and Integrase

Combinatorial Chemistry & High Throughput Screening ◽

10.2174/1386207320666170615104703 ◽

2017 ◽

Vol 20 (8) ◽

Cited By ~ 11

Author(s):

Subhash Chander ◽

Rajan Kumar Pandey ◽

Ashok Penta ◽

Bhanwar Singh Choudhary ◽

Manish Sharma ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Docking ◽

Molecular Dynamics Simulation ◽

Reverse Transcriptase ◽

Dynamics Simulation ◽

Dual Inhibitor ◽

Simulation Based ◽

Hiv 1

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Three-dimensional structure of HIV-1 VIF constructed by comparative modeling and the function characterization analyzed by molecular dynamics simulation

Organic & Biomolecular Chemistry ◽

10.1039/b612050d ◽

2007 ◽

Vol 5 (4) ◽

pp. 617 ◽

Cited By ~ 21

Author(s):

Wei Lv ◽

Zhenming Liu ◽

Hongwei Jin ◽

Xianghui Yu ◽

Liangren Zhang ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Three Dimensional ◽

Comparative Modeling ◽

Dynamics Simulation ◽

Dimensional Structure ◽

Three Dimensional Structure ◽

Function Characterization ◽

Hiv 1

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Effects of Urea, Tetramethyl Urea, and TrimethylamineN-Oxide on Aqueous Solution Structure and Solvation of Protein Backbones: A Molecular Dynamics Simulation Study

The Journal of Physical Chemistry B ◽

10.1021/jp9084926 ◽

2010 ◽

Vol 114 (1) ◽

pp. 557-568 ◽

Cited By ~ 128

Author(s):

Haiyan Wei ◽

Yubo Fan ◽

Yi Qin Gao

Keyword(s):

Molecular Dynamics ◽

Aqueous Solution ◽

Molecular Dynamics Simulation ◽

Simulation Study ◽

Solution Structure ◽

Dynamics Simulation ◽

Protein Backbones

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Molecular-dynamics simulation of avalanche in adhesion in a two-dimensional solid

Physical Review B ◽

10.1103/physrevb.45.13733 ◽

1992 ◽

Vol 45 (23) ◽

pp. 13733-13736 ◽

Cited By ~ 7

Author(s):

Mark Lupkowski ◽

John F. Maguire

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Two Dimensional

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Molecular dynamics simulation of HIV-1 protease in a crystalline environment and in solution. [Erratum to document cited in CA118(21):208404x]

Biochemistry ◽

10.1021/bi00063a035 ◽

1993 ◽

Vol 32 (12) ◽

pp. 3196-3196 ◽

Cited By ~ 2

Author(s):

D. M. York ◽

T. A. Darden ◽

L. G. Pedersen ◽

M. W. Anderson

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Crystalline Environment ◽

Hiv 1

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Nanovoids in uniaxially elongated polymer network filled with polydisperse nanoparticles via coarse-grained molecular dynamics simulation and two-dimensional scattering patterns

Polymer ◽

10.1016/j.polymer.2019.04.040 ◽

2019 ◽

Vol 174 ◽

pp. 218-233

Author(s):

Katsumi Hagita

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Polymer Network ◽

Dynamics Simulation ◽

Coarse Grained ◽

Two Dimensional ◽

Coarse Grained Molecular Dynamics

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