Key Interacting Residues between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamics Simulation and Density Functional Calculation

Bahaa Jawad; Puja Adhikari; Rudolf Podgornik; Wai-Yim Ching

doi:10.1021/acs.jcim.1c00560

Key Interacting Residues between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamics Simulation and Density Functional Calculation

Journal of Chemical Information and Modeling ◽

10.1021/acs.jcim.1c00560 ◽

2021 ◽

Vol 61 (9) ◽

pp. 4425-4441 ◽

Cited By ~ 1

Author(s):

Bahaa Jawad ◽

Puja Adhikari ◽

Rudolf Podgornik ◽

Wai-Yim Ching

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Density Functional ◽

Dynamics Simulation ◽

Density Functional Calculation

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An Application of Classical Molecular Dynamics Simulation and AB Initio Density-Functional Calculation in Surface Physics

Molecular Simulation ◽

10.1080/08927029408023036 ◽

1994 ◽

Vol 12 (3-6) ◽

pp. 271-289 ◽

Cited By ~ 5

Author(s):

H. Rafii-Tabar ◽

H. Kamiyama ◽

Y. Maruyama ◽

K. Ohno ◽

Y. Kawazoe

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Ab Initio ◽

Density Functional ◽

Dynamics Simulation ◽

Surface Physics ◽

Density Functional Calculation ◽

Classical Molecular Dynamics

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Investigation of Corrosion Inhibitors Adsorption on Metals Using Density Functional Theory and Molecular Dynamics Simulation

Corrosion Inhibitors ◽

10.5772/intechopen.84126 ◽

2019 ◽

Cited By ~ 1

Author(s):

Ambrish Singh ◽

Kashif R. Ansari ◽

Mumtaz A. Quraishi ◽

Yuanhua Lin

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Molecular Dynamics Simulation ◽

Density Functional ◽

Corrosion Inhibitors ◽

Dynamics Simulation ◽

Functional Theory

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Molecular docking and molecular dynamics simulation studies to identify potent AURKA inhibitors: assessing the performance of density functional theory, MM-GBSA and mass action kinetics calculations

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2019.1674695 ◽

2019 ◽

Vol 38 (14) ◽

pp. 4325-4335 ◽

Cited By ~ 6

Author(s):

Sathishkumar Chinnasamy ◽

Gurudeeban Selvaraj ◽

Aman Chandra Kaushik ◽

Satyavani Kaliamurthi ◽

Selvaraj Chandrabose ◽

...

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Molecular Docking ◽

Molecular Dynamics Simulation ◽

Density Functional ◽

Mass Action ◽

Dynamics Simulation ◽

Simulation Studies ◽

Functional Theory ◽

Mass Action Kinetics

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Molecular dynamics simulation of formamide in water using density functional theory and classical potentials

The Journal of Chemical Physics ◽

10.1063/1.479299 ◽

1999 ◽

Vol 111 (3) ◽

pp. 1117-1125 ◽

Cited By ~ 32

Author(s):

S. Chalmet ◽

M. F. Ruiz-López

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Molecular Dynamics Simulation ◽

Density Functional ◽

Dynamics Simulation ◽

Functional Theory

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Density Functional Theory and Molecular Dynamics Simulation of Poly(dimethylsiloxane) Melts near Silica Surfaces

Macromolecules ◽

10.1021/ma051001k ◽

2005 ◽

Vol 38 (20) ◽

pp. 8562-8573 ◽

Cited By ~ 5

Author(s):

Shyamal K. Nath ◽

Amalie L. Frischknecht ◽

John G. Curro ◽

John D. McCoy

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Molecular Dynamics Simulation ◽

Density Functional ◽

Dynamics Simulation ◽

Functional Theory ◽

Silica Surfaces

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A New Synthesized Schiff Base as Corrosion Inhibitor for Mild Steel in a HCl Medium: Experimental, Density Functional Theory and Molecular Dynamics Simulation Studies

Portugaliae Electrochimica Acta ◽

10.4152/pea.2021390504 ◽

2021 ◽

Vol 39 (5) ◽

pp. 349-379

Author(s):

I Kaabi ◽

T Douadi ◽

D Daoud ◽

S Amamra ◽

S Chafaa

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Schiff Base ◽

Molecular Dynamics Simulation ◽

Density Functional ◽

Dynamics Simulation ◽

Simulation Studies ◽

Functional Theory ◽

Experimental Density ◽

Hcl Medium

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Efficient Free-Energy Calculation of Proton Transfer by Constrained Density Functional Theory and Geometrically Restrained Molecular Dynamics Simulation

Chemistry Letters ◽

10.1246/cl.210132 ◽

2021 ◽

Author(s):

Tatsuya Joutsuka ◽

Koji Ando

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Proton Transfer ◽

Density Functional ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Functional Theory

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Quantum mechanical/molecular mechanical trajectory surface hopping molecular dynamics simulation by spin-flip time-dependent density functional theory

The Journal of Chemical Physics ◽

10.1063/1.5132879 ◽

2020 ◽

Vol 152 (2) ◽

pp. 024119 ◽

Cited By ~ 1

Author(s):

Noriyuki Minezawa ◽

Takahito Nakajima

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Molecular Dynamics Simulation ◽

Density Functional ◽

Time Dependent ◽

Dynamics Simulation ◽

Quantum Mechanical ◽

Functional Theory ◽

Surface Hopping ◽

Dependent Density

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Studies on the Encapsulation of Various Anions in Different Fullerenes Using Density Functional Theory Calculations and Born–Oppenheimer Molecular Dynamics Simulation

The Journal of Physical Chemistry A ◽

10.1021/jp203421v ◽

2011 ◽

Vol 115 (42) ◽

pp. 11723-11733 ◽

Cited By ~ 16

Author(s):

Pawar Ravinder ◽

Venkatesan Subramanian

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Molecular Dynamics Simulation ◽

Density Functional ◽

Density Functional Theory Calculations ◽

Dynamics Simulation ◽

Functional Theory

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Using a monomer potential energy surface to perform approximate path integral molecular dynamics simulation of ab initio water at near-zero added cost

Physical Chemistry Chemical Physics ◽

10.1039/c8cp06077k ◽

2019 ◽

Vol 21 (1) ◽

pp. 409-417 ◽

Cited By ~ 1

Author(s):

Daniel C. Elton ◽

Michelle Fritz ◽

Marivi Fernández-Serra

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Molecular Dynamics Simulation ◽

Potential Energy ◽

Path Integral ◽

Liquid Water ◽

Density Functional ◽

Energy Surface ◽

Dynamics Simulation ◽

Functional Theory

We present a new approximate method for doing path integral molecular dynamics simulation with density functional theory and show the utility of the method for liquid water.

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