Design and application of implicit solvent models in biomolecular simulations.
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.
Division of Mathematical Biology, MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, United Kingdom.
Jens
J
Kleinjung
Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, London SE1 1UL, United Kingdom. Electronic address: franca.fraternali@kcl.ac.uk.
Franca
F
Fraternali
D002462:Cell Membrane / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D009696:Nucleic Acids / Q000737:chemistry / Q000378:metabolism; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D012997:Solvents; D013816:Thermodynamics
D009696:Nucleic Acids; D011506:Proteins; D012997:Solvents