Unraveling the Coupling between Conformational Changes and Ligand Binding in Ribose Binding Protein Using Multiscale Molecular Dynamics and Free-Energy Calculations

2021 ◽  
Author(s):  
Weitong Ren ◽  
Hisham M. Dokainish ◽  
Ai Shinobu ◽  
Hiraku Oshima ◽  
Yuji Sugita
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ligand Binding ◽  
Conformational Changes ◽  
Binding Protein ◽  
Free Energy Calculations ◽  
Energy Calculations ◽  
Ribose Binding Protein

scholarly journals Insight into the Binding of DFG-out Allosteric Inhibitors to B-Raf Kinase Using Molecular Dynamics and Free Energy Calculations

2015 ◽  
Vol 11 (2) ◽  
pp. 124-136 ◽  
Author(s):  
Luis Coronel ◽  
Jose Granadino-Roldán ◽  
Marta Pinto ◽  
Maria Tomas ◽  
Maria Pujol ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Free Energy Calculations ◽  
Allosteric Inhibitors ◽  
Energy Calculations ◽  
Raf Kinase ◽  
Insight Into

scholarly journals Alchemical Absolute Protein-Ligand Binding Free Energies for Drug Design

2021 ◽  
Author(s):  
Yuriy Khalak ◽  
Gary Tresdern ◽  
Matteo Aldeghi ◽  
Hannah Magdalena Baumann ◽  
David L. Mobley ◽  
...  
Keyword(s):  
Free Energy ◽  
Drug Discovery ◽  
Drug Design ◽  
Ligand Binding ◽  
Binding Free Energy ◽  
Free Energy Calculations ◽  
Free Energies ◽  
Energy Calculations ◽  
Binding Free Energy Calculations ◽  
Binding Free Energies

The recent advances in relative protein-ligand binding free energy calculations have shown the value of alchemical methods in drug discovery. Accurately assessing absolute binding free energies, although highly desired, remains...

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