scholarly journals Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

2015 ◽  
Vol 137 (7) ◽  
pp. 2695-2703 ◽  
Author(s):  
Lingle Wang ◽  
Yujie Wu ◽  
Yuqing Deng ◽  
Byungchan Kim ◽  
Levi Pierce ◽  
...  
Keyword(s):  
Free Energy ◽  
Drug Discovery ◽  
Ligand Binding ◽  
Force Field ◽  
Free Energy Calculation ◽  
Energy Calculation ◽  
Reliable Prediction

scholarly journals Implementation of the QUBE Force Field for High-Throughput Alchemical Free Energy Calculations

2020 ◽  
Author(s):  
Lauren Nelson ◽  
Sofia Bariami ◽  
Chris Ringrose ◽  
Joshua Horton ◽  
Vadiraj Kurdekar ◽  
...  
Keyword(s):  
Free Energy ◽  
Force Field ◽  
High Throughput ◽  
Potential Energy Function ◽  
Free Energy Calculations ◽  
Dynamics Simulation ◽  
Free Energy Calculation ◽  
Energy Calculation ◽  
Alchemical Free Energy ◽  
Simulation Package

<div><div><div><p>The quantum mechanical bespoke (QUBE) force field approach has been developed to facilitate the automated derivation of potential energy function parameters for modelling protein-ligand binding. To date the approach has been validated in the context of Monte Carlo simulations of protein-ligand complexes. We describe here the implementation of the QUBE force field in the alchemical free energy calculation molecular dynamics simulation package SOMD. The implementation is validated by computing relative binding free energies for two congeneric series of non-nucleoside inhibitors of HIV-1 reverse transcriptase using QUBE and AMBER/GAFF force fields. The availability of QUBE in a modern simulation package that makes efficient use of GPU acceleration will greatly facilitate future high-throughput alchemical free energy calculation studies.</p></div></div></div>

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