Detachment of HCO3– from the Active Site of Carbonic Anhydrase: Molecular Dynamics Simulation and Machine Learning

2018 ◽  
Vol 122 (35) ◽  
pp. 20539-20549 ◽  
Author(s):  
Gong Chen ◽  
Diannan Lu ◽  
Jianzhong Wu ◽  
Zheng Liu
Keyword(s):  
Machine Learning ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Carbonic Anhydrase ◽  
Active Site ◽  
Dynamics Simulation

Machine Learning Interatomic Potentials for Global Optimization and Molecular Dynamics Simulation

2019 ◽  
pp. 253-288 ◽  
Author(s):  
Ivan A. Kruglov ◽  
Pavel E. Dolgirev ◽  
Artem R. Oganov ◽  
Arslan B. Mazitov ◽  
Sergey N. Pozdnyakov ◽  
...  
Keyword(s):  
Machine Learning ◽  
Molecular Dynamics ◽  
Global Optimization ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Interatomic Potentials

scholarly journals Molecular Docking and Molecular Dynamics Studies of SARS-CoV-2 Inhibitors: Crocin, Digitoxigenin, Beta-Eudesmol and Favipiravir: Comparative Study

2021 ◽  
Vol 12 (4) ◽  
pp. 5591-5600
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Comparative Study ◽  
Active Site ◽  
Antiviral Treatment ◽  
Docking Study ◽  
The Other ◽  
Dynamics Simulation ◽  
Main Protease

In this study, Crocin, Digitoxigenin, Beta-Eudesmol, and Favipiravir were docked in the active site of SARS-CoV-2 main protease (PDB code: 6LU7). The docking study was followed by Molecular Dynamics simulation. The result indicates that Crocin and Digitoxigenin are the structures with the best affinity in the studied enzyme's binding site. Still, Molecular Dynamics simulation showed that Digitoxigenin is the molecule that fits better in the active site of the main protease. Therefore, this molecule could have a more potent antiviral treatment of COVID-19 than the other three studied compounds.

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