Design and application of implicit solvent models in biomolecular simulations

J Kleinjung, F Fraternali - Current opinion in structural biology, 2014 - Elsevier
Current opinion in structural biology, 2014Elsevier
Highlights•Implicit solvent replaces explicit water by a potential of mean force.•Popular
models are SASA, VOL and Generalized Born.•Implicit solvent is used in MD, protein
modelling, folding, design, prediction and drug screening.•Large-scale simulations allow for
parametrisation via force matching.•Application to nucleic acids and membranes is
challenging.We review implicit solvent models and their parametrisation by introducing the
concepts and recent devlopments of the most popular models with a focus on …
Highlights
  • Implicit solvent replaces explicit water by a potential of mean force.
  • Popular models are SASA, VOL and Generalized Born.
  • Implicit solvent is used in MD, protein modelling, folding, design, prediction and drug screening.
  • Large-scale simulations allow for parametrisation via force matching.
  • Application to nucleic acids and membranes is challenging.
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.
Elsevier
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