Generalized Born Implicit Solvent Models for Biomolecules

Alexey V. Onufriev, David A. Case

Research output: Contribution to journalReview articlepeer-review

65 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)275-296
Number of pages22
JournalAnnual Review of Biophysics
Volume48
DOIs
StatePublished - May 6 2019

All Science Journal Classification (ASJC) codes

  • Biophysics
  • Structural Biology
  • Bioengineering
  • Biochemistry
  • Cell Biology

Keywords

  • biomolecular simulations
  • dielectric
  • electrostatics
  • generalized Born
  • implicit solvation

Fingerprint

Dive into the research topics of 'Generalized Born Implicit Solvent Models for Biomolecules'. Together they form a unique fingerprint.

Cite this