Design and application of implicit solvent models in biomolecular simulations

Curr Opin Struct Biol. 2014 Apr;25(100):126-34. doi: 10.1016/j.sbi.2014.04.003. Epub 2014 May 20.

Abstract

We review implicit solvent models and their parametrisation by introducing the concepts and recent devlopments of the most popular models with a focus on parametrisation via force matching. An overview of recent applications of the solvation energy term in protein dynamics, modelling, design and prediction is given to illustrate the usability and versatility of implicit solvation in reproducing the physical behaviour of biomolecular systems. Limitations of implicit modes are discussed through the example of more challenging systems like nucleic acids and membranes.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Cell Membrane / chemistry
  • Cell Membrane / metabolism
  • Models, Molecular*
  • Nucleic Acids / chemistry
  • Nucleic Acids / metabolism
  • Proteins / chemistry
  • Proteins / metabolism
  • Solvents*
  • Thermodynamics

Substances

  • Nucleic Acids
  • Proteins
  • Solvents