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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Detalles Bibliográficos
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
Descripción
Sumario: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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