Design and application of implicit solvent models in biomolecular simulations

•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.•Applicat...

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Veröffentlicht in:Current opinion in structural biology 2014-04, Vol.25 (100), p.126-134
Hauptverfasser: Kleinjung, Jens, Fraternali, Franca
Format: Artikel
Sprache:eng
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Zusammenfassung:•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.
ISSN:0959-440X
1879-033X
DOI:10.1016/j.sbi.2014.04.003