scholarly journals FEPrepare: A Web-Based Tool for Automating the Setup of Relative Binding Free Energy Calculations

2021 ◽  
Author(s):  
Stamatia Zavitsanou ◽  
Alexandros Tsengenes ◽  
Michail Papadourakis ◽  
Giorgio Amendola ◽  
Alexios Chatzigoulas ◽  
...  
Keyword(s):  
Free Energy ◽  
Binding Free Energy ◽  
Free Energy Calculations ◽  
Web Based ◽  
Energy Calculations ◽  
Relative Binding ◽  
Binding Free Energy Calculations

scholarly journals Relative Binding Free Energy Calculations Applied to Protein Homology Models

2016 ◽  
Vol 56 (12) ◽  
pp. 2388-2400 ◽  
Author(s):  
Daniel Cappel ◽  
Michelle Lynn Hall ◽  
Eelke B. Lenselink ◽  
Thijs Beuming ◽  
Jun Qi ◽  
...  
Keyword(s):  
Free Energy ◽  
Binding Free Energy ◽  
Free Energy Calculations ◽  
Protein Homology ◽  
Energy Calculations ◽  
Relative Binding ◽  
Binding Free Energy Calculations ◽  
Homology Models

scholarly journals A Benchmark of Electrostatic Methods Performance in Relative Binding Free Energy Calculations

2020 ◽  
Author(s):  
Yunhui Ge ◽  
David F. Hahn ◽  
David Mobley
Keyword(s):  
Free Energy ◽  
Early Stage ◽  
Binding Free Energy ◽  
Free Energy Calculations ◽  
Energy Calculations ◽  
Reaction Field ◽  
Know How ◽  
Particle Mesh Ewald ◽  
Relative Binding ◽  
Binding Free Energy Calculations

<div><div><div><p>Relative free energy calculations are fast becoming a critical part of early stage pharmaceu- tical design, making it important to know how to obtain the best performance with these calculations in applications which could span hundreds of calculations and molecules. In this work, we compared two different treatments of long-range electrostatics, Particle Mesh Ewald (PME) and Reaction Field (RF), in relative binding free energy calculations using a non-equilibrium switching protocol. We found simulations using RF achieve comparable re- sults as those using PME but gain more efficiency when using CPU and similar performance using GPU. The results from this work encourage more use of RF in molecular simulations.</p></div></div></div>

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