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 pre...

Descripción completa

Detalles Bibliográficos
Autores principales: Kleinjung, Jens, Fraternali, Franca
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier Science 2014
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4045398/
https://www.ncbi.nlm.nih.gov/pubmed/24841242
http://dx.doi.org/10.1016/j.sbi.2014.04.003
_version_ 1782319314473320448
author Kleinjung, Jens
Fraternali, Franca
author_facet Kleinjung, Jens
Fraternali, Franca
author_sort Kleinjung, Jens
collection PubMed
description 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.
format Online
Article
Text
id pubmed-4045398
institution National Center for Biotechnology Information
language English
publishDate 2014
publisher Elsevier Science
record_format MEDLINE/PubMed
spelling pubmed-40453982014-06-06 Design and application of implicit solvent models in biomolecular simulations Kleinjung, Jens Fraternali, Franca Curr Opin Struct Biol Article 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 Science 2014-04 /pmc/articles/PMC4045398/ /pubmed/24841242 http://dx.doi.org/10.1016/j.sbi.2014.04.003 Text en © 2014 The Authors http://creativecommons.org/licenses/by/3.0/ This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/3.0/).
spellingShingle Article
Kleinjung, Jens
Fraternali, Franca
Design and application of implicit solvent models in biomolecular simulations
title Design and application of implicit solvent models in biomolecular simulations
title_full Design and application of implicit solvent models in biomolecular simulations
title_fullStr Design and application of implicit solvent models in biomolecular simulations
title_full_unstemmed Design and application of implicit solvent models in biomolecular simulations
title_short Design and application of implicit solvent models in biomolecular simulations
title_sort design and application of implicit solvent models in biomolecular simulations
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4045398/
https://www.ncbi.nlm.nih.gov/pubmed/24841242
http://dx.doi.org/10.1016/j.sbi.2014.04.003
work_keys_str_mv AT kleinjungjens designandapplicationofimplicitsolventmodelsinbiomolecularsimulations
AT fraternalifranca designandapplicationofimplicitsolventmodelsinbiomolecularsimulations

Ejemplares similares