期刊
ANNUAL REVIEW OF BIOPHYSICS, VOL 48
卷 48, 期 -, 页码 275-296出版社
ANNUAL REVIEWS
DOI: 10.1146/annurev-biophys-052118-115325
关键词
electrostatics; dielectric; generalized Born; implicit solvation; biomolecular simulations
类别
资金
- NIGMS NIH HHS [R01 GM122086] Funding Source: Medline
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.
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