Generalized Born implicit solvent models for small molecule hydration free energies

2017 ◽  
Vol 19 (2) ◽  
pp. 1677-1685 ◽  
Author(s):  
Martin Brieg ◽  
Julia Setzler ◽  
Steffen Albert ◽  
Wolfgang Wenzel
Keyword(s):  
Free Energy ◽  
Small Molecules ◽  
Implicit Solvent ◽  
Free Energies ◽  
Hydration Free Energy ◽  
Energy Estimation ◽  
Generalized Born ◽  
Solvent Models ◽  
Molecular Force ◽  
Implicit Solvent Models

Hydration free energy estimation of small molecules from all-atom simulations was widely investigated in recent years, as it provides an essential test of molecular force fields and our understanding of solvation effects.

Examining Electrostatic Influences on Base-Flipping: A Comparison of TIP3P and GB Solvent Models

2013 ◽  
Vol 13 (1) ◽  
pp. 223-237 ◽  
Author(s):  
Allyn R. Brice ◽  
Brian N. Dominy
Keyword(s):  
Free Energy ◽  
Base Pair ◽  
Umbrella Sampling ◽  
Water Molecules ◽  
Implicit Solvent ◽  
Interaction Energies ◽  
Base Flipping ◽  
Solvent Models ◽  
Explicit Water ◽  
Implicit Solvent Models

AbstractRecently, it was demonstrated that implicit solvent models were capable of generating stable B-form DNA structures. Specifically, generalized Born (GB) implicit solvent models have improved regarding the solvation of conformational sampling of DNA [1,2]. Here, we examine the performance of the GBSW and GBMV models in CHARMM for characterizing base flipping free energy profiles of undamaged and damaged DNA bases. Umbrella sampling of the base flipping process was performed for the bases cytosine, uracil and xanthine. The umbrella sampling simulations were carried-out with both explicit (TIP3P) and implicit (GB) solvent in order to establish the impact of the solvent model on base flipping. Overall, base flipping potential of mean force (PMF) profiles generated with GB solvent resulted in a greater free energy difference of flipping than profiles generated with TIP3P. One of the significant differences between implicit and explicit solvent models is the approximation of solute-solvent interactions in implicit solvent models. We calculated electrostatic interaction energies between explicit water molecules and the base targeted for flipping. These interaction energies were calculated over the base flipping reaction coordinate to illustrate the stabilizing effect of the explicit water molecules on the flipped-out state. It is known that nucleic base pair hydrogen bonds also influenced the free energy of flipping since these favorable interactions must be broken in order for a base to flip-out of the helix. The Watson-Crick base pair hydrogen bond fractions were calculated over the umbrella sampling simulation windows in order to determine the effect of base pair interactions on the base flipping free energy. It is shown that interaction energies between the flipping base and explicit water molecules are responsible for the lower base flipping free energy difference in the explicit solvent PMF profiles.

scholarly journals Generalized Born Implicit Solvent Models for Biomolecules

2019 ◽  
Vol 48 (1) ◽  
pp. 275-296 ◽  
Author(s):  
Alexey V. Onufriev ◽  
David A. Case
Keyword(s):  
Md Simulations ◽  
Implicit Solvent ◽  
Molecular Mechanics Calculations ◽  
Generalized Born ◽  
Solvent Models ◽  
Explicit Consideration ◽  
Aqueous Solvation ◽  
Solvent Molecules ◽  
The Individual ◽  
Implicit Solvent Models

It would often be useful in computer simulations to use an implicit description of solvation effects, instead of explicitly representing the individual solvent molecules. Continuum dielectric models often work well in describing the thermodynamic aspects of aqueous solvation and can be very efficient compared to the explicit treatment of the solvent. Here, we review a particular class of so-called fast implicit solvent models, generalized Born (GB) models, which are widely used for molecular dynamics (MD) simulations of proteins and nucleic acids. These approaches model hydration effects and provide solvent-dependent forces with efficiencies comparable to molecular-mechanics calculations on the solute alone; as such, they can be incorporated into MD or other conformational searching strategies in a straightforward manner. The foundations of the GB model are reviewed, followed by examples of newer, emerging models and examples of important applications. We discuss their strengths and weaknesses, both for fidelity to the underlying continuum model and for the ability to replace explicit consideration of solvent molecules in macromolecular simulations.

scholarly journals Simulations of Surfactant and Lipid Assemblies with Generalized Born Implicit Solvent Models

2010 ◽  
Vol 98 (3) ◽  
pp. 486a ◽  
Author(s):  
Jana K. Shen ◽  
Yuhang Wang ◽  
Jason A. Wallace ◽  
Peter Koenig
Keyword(s):  
Implicit Solvent ◽  
Generalized Born ◽  
Solvent Models ◽  
Lipid Assemblies ◽  
Implicit Solvent Models

scholarly journals Electrostatic Free Energy and Its Variations in Implicit Solvent Models

2008 ◽  
Vol 112 (10) ◽  
pp. 3058-3069 ◽  
Author(s):  
Jianwei Che ◽  
Joachim Dzubiella ◽  
Bo Li ◽  
J. Andrew McCammon
Keyword(s):  
Free Energy ◽  
Implicit Solvent ◽  
Solvent Models ◽  
Electrostatic Free Energy ◽  
Implicit Solvent Models
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