scholarly journals Combining free energy calculations with tailored enzyme activity assays to elucidate substrate binding of a phospho-lysine phosphatase

2020 ◽  
Vol 11 (47) ◽  
pp. 12655-12661
Author(s):  
Anett Hauser ◽  
Songhwan Hwang ◽  
Han Sun ◽  
Christian P. R. Hackenberger
Keyword(s):  
Free Energy ◽  
Enzyme Activity ◽  
Molecular Docking ◽  
Phosphatase Activity ◽  
Substrate Binding ◽  
Free Energy Calculations ◽  
Energy Calculations

Combining phosphatase activity assays with molecular docking and free energy calculations reveals low promiscuity and substrate binding of intrinsically labile phospho-lysine peptides to the enzyme LHPP.

scholarly journals Free energy calculations elucidate substrate binding, gating mechanism, and tolerance‐promoting mutations in herbicide target 4‐hydroxyphenylpyruvate dioxygenase

2019 ◽  
Vol 28 (6) ◽  
pp. 1048-1058 ◽  
Author(s):  
Christina E. M. Schindler ◽  
Eva Hollenbach ◽  
Thomas Mietzner ◽  
Klaus‐Jürgen Schleifer ◽  
Martin Zacharias
Keyword(s):  
Free Energy ◽  
Substrate Binding ◽  
Free Energy Calculations ◽  
Energy Calculations ◽  
Gating Mechanism

scholarly journals Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset

2019 ◽  
Vol 33 (12) ◽  
pp. 1031-1043 ◽  
Author(s):  
Eddy Elisée ◽  
Vytautas Gapsys ◽  
Nawel Mele ◽  
Ludovic Chaput ◽  
Edithe Selwa ◽  
...  
Keyword(s):  
Free Energy ◽  
Performance Evaluation ◽  
Molecular Docking ◽  
Free Energy Calculations ◽  
Grand Challenge ◽  
Energy Calculations

scholarly journals Identification of Potential Binders of the SARS-Cov-2 Spike Protein via Molecular Docking, Dynamics Simulation and Binding Free Energy Calculation

2020 ◽  
Author(s):  
Dr. Chirag N. Patel ◽  
Dr. Prasanth Kumar S. ◽  
Dr. Himanshu A. Pandya ◽  
Dr. Rakesh M. Rawal
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Docking ◽  
Molecular Dynamics Simulations ◽  
Binding Free Energy ◽  
Free Energy Calculations ◽  
Dynamics Simulation ◽  
Spike Protein ◽  
Energy Calculations ◽  
Dynamics Simulations

<p>The pandemic outbreak of COVID-19 virus (SARS-CoV-2) has become critical global health issue. The biophysical and structural evidence shows that SARS-CoV-2 spike protein possesses higher binding affinity towards angiotensin-converting enzyme 2 (ACE2) and hemagglutinin-acetylesterase (HE) glycoprotein receptor. Hence, it was selected as a target to generate the potential candidates for the inhibition of HE glycoprotein. The present study focuses on extensive computational approaches which contains molecular docking, ADMET prediction followed by molecular dynamics simulations and free energy calculations. Furthermore, virtual screening of NPACT compounds identified 3,4,5-Trihydroxy-1,8-bis[(2R,3R)-3,5,7-trihydroxy-3,4-dihydro-2H-chromen-2-yl]benzo[7]annulen-6-one, Silymarin, Withanolide D, Spirosolane and Oridonin were interact with high affinity. The ADMET prediction revealed pharmacokinetics and drug-likeness properties of top-ranked compounds. Molecular dynamics simulations and binding free energy calculations affirmed that these five NPACT compounds were robust HE inhibitor.</p>

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