2016
DOI: 10.1002/jcc.24390
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Rapid approximate calculation of water binding free energies in the whole hydration domain of (bio)macromolecules

Abstract: The evaluation of water binding free energies around solute molecules is important for the thermodynamic characterization of hydration or association processes. Here, a rapid approximate method to estimate water binding free energies around (bio)macromolecules from a single molecular dynamics simulation is presented. The basic idea is that endpoint free-energy calculation methods are applied and the endpoint quantities are monitored on a three-dimensional grid around the solute. Thus, a gridded map of water bi… Show more

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Cited by 3 publications
(3 citation statements)
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“…Illustration of water binding free energy in the vicinity of the a) monomeric and b) dimeric solute molecules. The calculation is based on a linear interaction energy approach . Blue color represents favorable binding of water while red color represents unfavorable interaction.…”
Section: Thermodynamic Driving Forces For Self‐assemblymentioning
confidence: 99%
“…Illustration of water binding free energy in the vicinity of the a) monomeric and b) dimeric solute molecules. The calculation is based on a linear interaction energy approach . Blue color represents favorable binding of water while red color represents unfavorable interaction.…”
Section: Thermodynamic Driving Forces For Self‐assemblymentioning
confidence: 99%
“…Various methods exist for the calculation of free energy differences from MD. When only liquids and solids are involved as is the case here, we can work with the Helmholtz free energy and consider constant temperature ( T ) and volume ( V ) conditions. For the problem in hand, it is best to obtain the free energy directly from the averaged forces.…”
mentioning
confidence: 99%
“…At constant temperature, when 1 mol water is removed from the material, the additional energy is called binding energy after removing latent heat of vaporization [22,23] , which is evaluated by Equation ( 4):…”
Section: Thermodynamic Properties 241 Binding Energymentioning
confidence: 99%