Studying Interactions by Molecular Dynamics Simulations at High Concentration

Molecular dynamics simulations have been used to study molecular encounters and recognition. In recent works, simulations using high concentration of interacting molecules have been performed. In this paper, we consider the practical problems for setting up the simulation and to analyse the results...

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Autores principales: Fogolari, Federico, Corazza, Alessandra, Toppo, Stefano, Tosatto, Silvio C. E., Viglino, Paolo, Ursini, Fulvio, Esposito, Gennaro
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2012
Materias:
Methodology Report
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303702/
https://www.ncbi.nlm.nih.gov/pubmed/22500085
http://dx.doi.org/10.1155/2012/303190
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author Fogolari, Federico
Corazza, Alessandra
Toppo, Stefano
Tosatto, Silvio C. E.
Viglino, Paolo
Ursini, Fulvio
Esposito, Gennaro
author_facet Fogolari, Federico
Corazza, Alessandra
Toppo, Stefano
Tosatto, Silvio C. E.
Viglino, Paolo
Ursini, Fulvio
Esposito, Gennaro
author_sort Fogolari, Federico
collection PubMed
description Molecular dynamics simulations have been used to study molecular encounters and recognition. In recent works, simulations using high concentration of interacting molecules have been performed. In this paper, we consider the practical problems for setting up the simulation and to analyse the results of the simulation. The simulation of beta 2-microglobulin association and the simulation of the binding of hydrogen peroxide by glutathione peroxidase are provided as examples.
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spelling pubmed-33037022012-04-12 Studying Interactions by Molecular Dynamics Simulations at High Concentration Fogolari, Federico Corazza, Alessandra Toppo, Stefano Tosatto, Silvio C. E. Viglino, Paolo Ursini, Fulvio Esposito, Gennaro J Biomed Biotechnol Methodology Report Molecular dynamics simulations have been used to study molecular encounters and recognition. In recent works, simulations using high concentration of interacting molecules have been performed. In this paper, we consider the practical problems for setting up the simulation and to analyse the results of the simulation. The simulation of beta 2-microglobulin association and the simulation of the binding of hydrogen peroxide by glutathione peroxidase are provided as examples. Hindawi Publishing Corporation 2012 2012-02-22 /pmc/articles/PMC3303702/ /pubmed/22500085 http://dx.doi.org/10.1155/2012/303190 Text en Copyright © 2012 Federico Fogolari et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Methodology Report
Fogolari, Federico
Corazza, Alessandra
Toppo, Stefano
Tosatto, Silvio C. E.
Viglino, Paolo
Ursini, Fulvio
Esposito, Gennaro
Studying Interactions by Molecular Dynamics Simulations at High Concentration
title Studying Interactions by Molecular Dynamics Simulations at High Concentration
title_full Studying Interactions by Molecular Dynamics Simulations at High Concentration
title_fullStr Studying Interactions by Molecular Dynamics Simulations at High Concentration
title_full_unstemmed Studying Interactions by Molecular Dynamics Simulations at High Concentration
title_short Studying Interactions by Molecular Dynamics Simulations at High Concentration
title_sort studying interactions by molecular dynamics simulations at high concentration
topic Methodology Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303702/
https://www.ncbi.nlm.nih.gov/pubmed/22500085
http://dx.doi.org/10.1155/2012/303190
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