Use of MM-PBSA in Reproducing the Binding Free Energies to HIV-1 RT of TIBO Derivatives and Predicting the Binding Mode to HIV-1 RT of Efavirenz by Docking and MM-PBSA

2001 ◽  
Vol 123 (22) ◽  
pp. 5221-5230 ◽  
Author(s):  
Junmei Wang ◽  
Paul Morin ◽  
Wei Wang ◽  
Peter A. Kollman
Keyword(s):  
Binding Mode ◽  
Free Energies ◽  
Hiv 1 ◽  
Binding Free Energies

scholarly journals Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors

2014 ◽  
Vol 10 (3) ◽  
pp. 1228-1241 ◽  
Author(s):  
David W. Wright ◽  
Benjamin A. Hall ◽  
Owain A. Kenway ◽  
Shantenu Jha ◽  
Peter V. Coveney
Keyword(s):  
Protease Inhibitors ◽  
Free Energies ◽  
Hiv 1 ◽  
Binding Free Energies

Comparison of the Molecular Dynamics and Calculated Binding Free Energies for Nine FDA-Approved HIV-1 PR Drugs Against Subtype B and C-SA HIV PR

2012 ◽  
Vol 81 (2) ◽  
pp. 208-218 ◽  
Author(s):  
Shaimaa M. Ahmed ◽  
Hendrik G. Kruger ◽  
Thirumala Govender ◽  
Glenn E. M. Maguire ◽  
Yasien Sayed ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energies ◽  
Subtype B ◽  
Hiv 1 ◽  
Binding Free Energies

Studies on binding free energies and the binding mode by docking and MM-PBSA in gp41-ligand complex

2005 ◽  
Vol 31 (14-15) ◽  
pp. 1051-1056 ◽  
Author(s):  
J. J. TAN ◽  
R. KONG ◽  
W. Z. CHEN ◽  
C. X. WANG
Keyword(s):  
Binding Mode ◽  
Free Energies ◽  
Ligand Complex ◽  
Binding Free Energies

Rapid and Accurate Prediction of Binding Free Energies for Saquinavir-Bound HIV-1 Proteases

2008 ◽  
Vol 130 (8) ◽  
pp. 2639-2648 ◽  
Author(s):  
Ileana Stoica ◽  
S. Kashif Sadiq ◽  
Peter V. Coveney
Keyword(s):  
Accurate Prediction ◽  
Free Energies ◽  
Hiv 1 ◽  
Binding Free Energies

scholarly journals Exploring the binding mode and thermodynamics of inverse agonists against estrogen-related receptor alpha

RSC Advances ◽  
2020 ◽  
Vol 10 (28) ◽  
pp. 16659-16668 ◽  
Author(s):  
Konda Reddy Karnati ◽  
Yixuan Wang ◽  
Yongli Du
Keyword(s):  
Md Simulations ◽  
Binding Mode ◽  
Free Energies ◽  
Inverse Agonists ◽  
Receptor Alpha ◽  
First Time ◽  
Estrogen Related Receptor ◽  
Binding Free Energies

All-atom MD simulations were for the first time carried out for the complexes of inverse agonists and ERRα, and their binding free energies were also calculated with MM-PBSA to quantitatively discuss the binding of the inverse agonists with ERRα.

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