1. Studying Interactions by Molecular Dynamics Simulations at High Concentration.
- Author
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Fogolari, Federico, Corazza, Alessandra, Toppo, Stefano, Tosatto, Silvio C. E., Viglino, Paolo, Ursini, Fulvio, and Esposito, Gennaro
- Subjects
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COMPUTER simulation , *ALGORITHMS , *DIFFUSION , *HYDROGEN peroxide , *MOLECULAR biology , *OXIDOREDUCTASES , *RESEARCH funding , *BETA globulins , *DATA analysis software , *STATISTICAL models , *DESCRIPTIVE statistics - 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. [ABSTRACT FROM AUTHOR]
- Published
- 2012
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