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

Research output: Contribution to journalArticle

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 languageEnglish (US)
Article number303190
JournalJournal of Biomedicine and Biotechnology
Volume2012
DOIs
StatePublished - 2012

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Medicine
  • Molecular Biology
  • Genetics
  • Health, Toxicology and Mutagenesis

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