Decomposition of the Solvation Free Energies of Deoxyribonucleoside Triphosphates Using the Free Energy Perturbation Method

2006 ◽  
Vol 110 (25) ◽  
pp. 12782-12788 ◽  
Author(s):  
Urban Bren ◽  
Václav Martínek ◽  
Jan Florián
Keyword(s):  
Free Energy ◽  
Perturbation Method ◽  
Free Energy Perturbation ◽  
Free Energies ◽  
Energy Perturbation ◽  
Solvation Free Energies

Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field

2010 ◽  
Vol 6 (5) ◽  
pp. 1509-1519 ◽  
Author(s):  
Devleena Shivakumar ◽  
Joshua Williams ◽  
Yujie Wu ◽  
Wolfgang Damm ◽  
John Shelley ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Force Field ◽  
Free Energy Perturbation ◽  
Free Energies ◽  
Energy Perturbation ◽  
Solvation Free Energies

Advances in Binding Free Energies Calculations: QM/MM-Based Free Energy Perturbation Method for Drug Design

2013 ◽  
Vol 19 (26) ◽  
pp. 4674-4686 ◽  
Author(s):  
R.S. Rathore ◽  
M. Sumakanth ◽  
M. Reddy ◽  
P. Reddanna ◽  
Allam Rao ◽  
...  
Keyword(s):  
Free Energy ◽  
Drug Design ◽  
Perturbation Method ◽  
Free Energy Perturbation ◽  
Free Energies ◽  
Energy Perturbation ◽  
Binding Free Energies

scholarly journals Solvation free energies via alchemical simulations: let's get honest about sampling, once more

2019 ◽  
Vol 21 (25) ◽  
pp. 13826-13834 ◽  
Author(s):  
Piero Procacci
Keyword(s):  
Free Energy ◽  
Free Energy Perturbation ◽  
Computational Studies ◽  
Free Energies ◽  
Biologically Relevant ◽  
Energy Perturbation ◽  
Biologically Relevant Molecules ◽  
Solvation Free Energies

Free energy perturbation (FEP) approaches with stratification have seen widespread and increasing use in computational studies of biologically relevant molecules.

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