Studying interactions by molecular dynamics simulations at high concentration

Federico Fogolari; Alessandra Corazza; Stefano Toppo; Silvio C.E. Tosatto; Paolo Viglino; Fulvio Ursini; Gennaro Esposito

doi:10.1155/2012/303190

Studying interactions by molecular dynamics simulations at high concentration

Federico Fogolari, Alessandra Corazza, Stefano Toppo, Silvio C.E. Tosatto, Paolo Viglino, Fulvio Ursini, Gennaro Esposito

Chemistry

Research output: Contribution to journal › Article › peer-review

Abstract

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.

Original language	English (US)
Article number	303190
Journal	Journal of Biomedicine and Biotechnology
Volume	2012
DOIs	https://doi.org/10.1155/2012/303190
State	Published - 2012

ASJC Scopus subject areas

Biotechnology
Molecular Medicine
Molecular Biology
Genetics
Health, Toxicology and Mutagenesis

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10.1155/2012/303190

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abstract = "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.",

author = "Federico Fogolari and Alessandra Corazza and Stefano Toppo and Tosatto, {Silvio C.E.} and Paolo Viglino and Fulvio Ursini and Gennaro Esposito",

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AU - Fogolari, Federico

AU - Corazza, Alessandra

AU - Toppo, Stefano

AU - Tosatto, Silvio C.E.

AU - Viglino, Paolo

AU - Ursini, Fulvio

AU - Esposito, Gennaro

PY - 2012

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AB - 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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Studying interactions by molecular dynamics simulations at high concentration

Abstract

ASJC Scopus subject areas

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