Studying Interactions by Molecular Dynamics Simulations at High Concentration

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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Main Authors: Federico Fogolari, Alessandra Corazza, Stefano Toppo, Silvio C. E. Tosatto, Paolo Viglino, Fulvio Ursini, Gennaro Esposito
Format: Article
Language:English
Published: Hindawi Limited 2012-01-01
Series:Journal of Biomedicine and Biotechnology
Online Access:http://dx.doi.org/10.1155/2012/303190
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spelling doaj-74ce78f67cfe4576818bfeb14d6c111b2020-11-24T22:03:11ZengHindawi LimitedJournal of Biomedicine and Biotechnology1110-72431110-72512012-01-01201210.1155/2012/303190303190Studying Interactions by Molecular Dynamics Simulations at High ConcentrationFederico Fogolari0Alessandra Corazza1Stefano Toppo2Silvio C. E. Tosatto3Paolo Viglino4Fulvio Ursini5Gennaro Esposito6Dipartimento di Scienze Mediche e Biologiche, Università di Udine, Piazzale Kolbe 4, 33100 Udine, ItalyDipartimento di Scienze Mediche e Biologiche, Università di Udine, Piazzale Kolbe 4, 33100 Udine, ItalyDipartimento di Chimica Biologica, Università di Padova, Viale G. Colombo 3, 35121 Padova, ItalyDipartimento di Biologia, Università di Padova, Viale G. Colombo 3, 35121 Padova, ItalyDipartimento di Scienze Mediche e Biologiche, Università di Udine, Piazzale Kolbe 4, 33100 Udine, ItalyDipartimento di Chimica Biologica, Università di Padova, Viale G. Colombo 3, 35121 Padova, ItalyDipartimento di Scienze Mediche e Biologiche, Università di Udine, Piazzale Kolbe 4, 33100 Udine, ItalyMolecular 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.http://dx.doi.org/10.1155/2012/303190
collection DOAJ
language English
format Article
sources DOAJ
author Federico Fogolari
Alessandra Corazza
Stefano Toppo
Silvio C. E. Tosatto
Paolo Viglino
Fulvio Ursini
Gennaro Esposito
spellingShingle Federico Fogolari
Alessandra Corazza
Stefano Toppo
Silvio C. E. Tosatto
Paolo Viglino
Fulvio Ursini
Gennaro Esposito
Studying Interactions by Molecular Dynamics Simulations at High Concentration
Journal of Biomedicine and Biotechnology
author_facet Federico Fogolari
Alessandra Corazza
Stefano Toppo
Silvio C. E. Tosatto
Paolo Viglino
Fulvio Ursini
Gennaro Esposito
author_sort Federico Fogolari
title Studying Interactions by Molecular Dynamics Simulations at High Concentration
title_short 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_sort studying interactions by molecular dynamics simulations at high concentration
publisher Hindawi Limited
series Journal of Biomedicine and Biotechnology
issn 1110-7243
1110-7251
publishDate 2012-01-01
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.
url http://dx.doi.org/10.1155/2012/303190
work_keys_str_mv AT federicofogolari studyinginteractionsbymoleculardynamicssimulationsathighconcentration
AT alessandracorazza studyinginteractionsbymoleculardynamicssimulationsathighconcentration
AT stefanotoppo studyinginteractionsbymoleculardynamicssimulationsathighconcentration
AT silviocetosatto studyinginteractionsbymoleculardynamicssimulationsathighconcentration
AT paoloviglino studyinginteractionsbymoleculardynamicssimulationsathighconcentration
AT fulvioursini studyinginteractionsbymoleculardynamicssimulationsathighconcentration
AT gennaroesposito studyinginteractionsbymoleculardynamicssimulationsathighconcentration
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