Prediction of the binding modes between macrolactin N and peptide deformylase from Staphylococcus aureus by molecular docking and molecular dynamics simulations

2012 ◽  
Vol 22 (6) ◽  
pp. 2889-2901 ◽  
Author(s):  
Jian Gao ◽  
Yuanhua Cheng ◽  
Wei Cui ◽  
Fushi Zhang ◽  
Huai Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Staphylococcus Aureus ◽  
Molecular Docking ◽  
Molecular Dynamics Simulations ◽  
Peptide Deformylase ◽  
Binding Modes ◽  
Dynamics Simulations

scholarly journals Comparison of Molecular Docking and Molecular Dynamics Simulations of 1,3-Thiazin-4-One with MDM2 Protein

2015 ◽  
Vol 60 ◽  
pp. 161-167 ◽  
Author(s):  
S. Athavan Alias Anand ◽  
C. Loganathan ◽  
K. Saravanan ◽  
S. Kabilan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulations ◽  
Binding Modes ◽  
Software Suite ◽  
Mdm2 Protein ◽  
Important Amino Acid ◽  
Dynamic Studies ◽  
Dynamics Simulations ◽  
Oncogene Protein

The molecular docking and molecular dynamics simulations studies of 1,3–thiazin–4–one derivative with a bonafide oncogene protein MDM2 (PDB ID: 4HBM) was investigated. Both the docking and dynamics simulations were performed in Schrödinger software suite 2014 using Glide and Desmond modules. The results of docking and dynamics were compared to investigate the possible binding modes of the thiazinone derivative with 4HBM. The tested molecule shows critical interactions with the important amino acid His 96 which is necessary for the inhibition of MDM2 in both docking and dynamic studies.

Promising inhibitors of nsp2 of CHIKV using molecular docking and temperature-dependent molecular dynamics simulations

2021 ◽  
pp. 1-9
Author(s):  
Mahendera Kumar Meena ◽  
Durgesh Kumar ◽  
Kamlesh Kumari ◽  
Nagendra Kumar Kaushik ◽  
Rammapa Venkatesh Kumar ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulations ◽  
Temperature Dependent ◽  
Dynamics Simulations
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